Low 5 In Uno Sold Box New Sneakers Alce Out 39 Buscemi Sneakers White RqwYEE Low 5 In Uno Sold Box New Sneakers Alce Out 39 Buscemi Sneakers White RqwYEE Low 5 In Uno Sold Box New Sneakers Alce Out 39 Buscemi Sneakers White RqwYEE Low 5 In Uno Sold Box New Sneakers Alce Out 39 Buscemi Sneakers White RqwYEE Low 5 In Uno Sold Box New Sneakers Alce Out 39 Buscemi Sneakers White RqwYEE Low 5 In Uno Sold Box New Sneakers Alce Out 39 Buscemi Sneakers White RqwYEE Low 5 In Uno Sold Box New Sneakers Alce Out 39 Buscemi Sneakers White RqwYEE Low 5 In Uno Sold Box New Sneakers Alce Out 39 Buscemi Sneakers White RqwYEE Low 5 In Uno Sold Box New Sneakers Alce Out 39 Buscemi Sneakers White RqwYEE Low 5 In Uno Sold Box New Sneakers Alce Out 39 Buscemi Sneakers White RqwYEE

Low 5 In Uno Sold Box New Sneakers Alce Out 39 Buscemi Sneakers White RqwYEE

 
When referencing this page, please use this url: http://blanco.biomol.uci.edu/mpstruc/
 

News        Subscribe for rss news updates

  • Membrane-embedded structures now available!: Mark Sansom's lab at Oxford has created the MemProtMD database of all known transmembrane proteins embedded in lipid membranes, described in Stansfeld et al. (2015) Structure 23:1350-1361. Links to the structures are now included in mpstruc. Click on the icon, and you will be taken to the appropriate entry in MemProtMD.
  • MPtopo XML data representations now available: XML representations are now available for the MPtopo membrane protein topology database.
  • MPtopo integrated into mpstruc: MPtopo, our curated database of membrane proteins with experimentally validated transmembrane segments, has a new structure and interface: It is now integrated with mpstruc (e.g., see the mpstruc entry for 2BRD for a link to mptopo). MPEx has also been updated to use the new mptopo.

Latest new protein entered: 28 八月 2018 at 19:22 PDT.
Last database update: 28 八月 2018 at 19:25 PDT

New Structures:
Unique proteins in database = 817
Coördinate files in database = 2619
Published reports of membrane protein structures in database = 1458
(Counts do not include pre-publication structures)
A full list of pdb codes currently in the database is available here.

Unique proteins include proteins of same type from different species. For example, photosynthetic reaction centers from R. viridis and R. sphaeroides are considered unique. Structures of mutagenized versions of proteins already in the database are excluded as unique. Proteins that differ only by substrate bound or by physiological state are also excluded. Structures 'obsoleted' by the PDB are not included.

Total number of PDB coördinate files, including those for unique proteins. This number reflects the fact that published reports of structures often include several coördinate files describing, for example, the protein in different crystal forms, or with different bound substrates.


Pre-Publication Structures (link to mpstruc bulletin board page)
 
A word about the new interface to the protein table.

There are other ways of viewing the data in the mpstruc database besides the hierarchical view presented in the table on this page. The mpstruc database queries page (follow the above link) provides a list of queries on the database, some of which provide tables with sortable columns. Some of the queries may take a few moments. Query results are also available as XML data.

Currently available queries include requesting a list of unique proteins, a list of all published reports, counting unique proteins by year, and counting all published reports by year.

XML Representations

An XML representation provides a convenient machine or human readable format of the portion of the data table that has been made visible, and allows you to build software tools to consume it as you see fit. You can use the URLs adjacent to the buttons below to access the same view the corresponding button provides.

This button generates an XML representation of the currently visible portion of the table.

//blanco.biomol.uci.edu/mpstruc/listAll/mpstrucTblXml
//blanco.biomol.uci.edu/mpstruc/listAll/mpstrucMonotopicTblXml
//blanco.biomol.uci.edu/mpstruc/listAll/mpstrucBetaBrlTblXml
//blanco.biomol.uci.edu/mpstruc/listAll/mpstrucAlphaHlxTblXml

If your browser doesn’t directly display a nicely formatted XML page, it should provide a "view page source" menu selection that will. It should also provide a "save page" option so that you can download the XML formatted data.

If you’re not familiar with XML and how to use it, a good source of information is available here.

NOTES:

Generated XML uses the following Document Type Definition (DTD):


  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
]>

 
Links to the Protein Data Bank Site
Links to the Structural Biology Knowledgebase Site
Membrane Proteins of Known 3D Structure
( Table description)
Protein
PDB Code Links Reference
(links are to PubMed)
MONOTOPIC MEMBRANE PROTEINS
Cyclooxygenases
Ram Prostaglandin H2 synthase-1 (cyclooxygenase-1 or COX-1): Ovis aries  E Eukaryota, 3.5 Å
Picot et al. (1994).
Picot D, Loll PJ, & Garavito RM (1994). The x-ray crystal structure of the membrane protein prostaglandin H 2synthase-1.
Nature 367 :243-249.
PubMed Id: 8121489.
Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries  E Eukaryota, 3.4 Å
In complex with bromoaspirin.
Loll et al. (1995).
Loll PJ, Picot D, & Garavito RM (1995). The structural basis of aspirin activity inferred from the crystal structure of inactivated prostaglandin H2 synthase.
Nat Struct Biol 2 :637-643.
PubMed Id: 7552725.
Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries  E Eukaryota, 3.1 Å
In complex with flurbiprofen.
Garavito et al. (1995).
Garavito RM, Picot D, & Loll PJ (1995). The 3.1 A X-ray crystal structure of the integral membrane enzyme prostaglandin H2 synthase-1.
Adv Prostaglandin Thromboxane Leukot Res 23 :99-103.
PubMed Id: 7732912.
Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries  E Eukaryota, 2.61 Å
1EQG is complex with ibuprofen.
Complex with flurbiprofen, 2.70 Å: 1EQH
Complex with flurbiprofen methyl ester, 2.75 Å: 1HT5
Complex with alclofenac, 2.69 Å: 1HT8
Selinsky et al. (2001).
Selinsky BS, Gupta K, Sharkey CT, Loll PJ (2001). Structural analysis of NSAID binding by prostaglandin H2 synthase: time-dependent and time-independent inhibitors elicit identical enzyme conformations.
Biochemistry 40 :5172-5180.
PubMed Id: 11318639.
Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries  E Eukaryota, 3.2 Å
In complex with O-actylsalicylhydroxamic acid.
Loll et al. (2001).
Loll PJ, Sharkey CT, O'Connor SJ, Dooley CM, O'Brien E, Devocelle M, Nolan KB, Selinsky BS, & Fitzgerald DJ (2001). O-acetylsalicylhydroxamic acid, a novel acetylating inhibitor of prostaglandin H2 synthase: structural and functional characterization of enzyme-inhibitor interactions.
Mol Pharmacol 60 :1407-1413.
PubMed Id: 11723249.
Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries  E Eukaryota, 2.00 Å
In complex with alpha-methyl-4-biphenyl acetic acid.
Gupta et al. (2004).
Gupta K, Selinsky BS, Kaub CJ, Katz AK, & Loll PJ (2004). The 2.0 Å resolution crystal structure of prostaglandin H2 synthase-1: structural insights into an unusual peroxidase.
J Mol Biol 335 :503-518.
PubMed Id: 14672659.
Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries  E Eukaryota, 2.00 Å
In complex with flurbiprofen + Mn(III) PPIX cofactor.
Gupta et al. (2006).
Gupta K, Selinsky BS, & Loll PJ (2006). 2.0 angstroms structure of prostaglandin H2 synthase-1 reconstituted with a manganese porphyrin cofactor.
Acta Crystallogr D Biol Crystallogr 62 :151-156.
PubMed Id: 16421446.
Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries  E Eukaryota (expressed in Spodoptera frugiperda), 3.05 Å
3N8V is the unoccupied structure.
R120Q/Native Heterodimer mutant in complex with Flurbiprofen, 2.75 Å: 3N8W
COX-1 in complex with Nimesulide, 2.75 Å: 3N8X
Aspirin Acetylated COX-1 in Complex with Diclofenac, 2.60 Å: 3N8Y
COX-1 in Complex with Flurbiprofen, 2.90 Å: 3N8Z
Sidhu et al. (2010).
Sidhu RS, Lee JY, Yuan C, & Smith WL (2010). Comparison of Cyclooxygenase-1 Crystal Structures: Cross-Talk between Monomers Comprising Cyclooxygenase-1 Homodimers.
Biochemistry 49 :7069-7079.
PubMed Id: 20669977.
Cyclooxygenase-2: Mus musculus  E Eukaryota, 3.0 Å
Kurumbail et al. (1996).
Kurumbail RG, Stevens AM, Gierse JK, McDonald JJ, Stegeman RA, Pak JY, Gildehaus D, Miyashiro JM, Penning TD, Seibert, K et al (1996). Structural basis for selective inhibition of cyclooxygenase-2 by anti-inflammatory agents.
Nature 384 :644-648.
PubMed Id: 8967954.
Fatty acid α-dioxygenase (α-DOX): Arabidopsis thaliana  E Eukaryota (expressed in E. coli), 1.70 Å
First structure of a member of the α-DOX subfamily of cyclooxygenase-perixidase family of heme-containing proteins.
With bound imidazole, 1.51 Å: 4HHR
Goulah et al. (2013).
Goulah CC, Zhu G, Koszelak-Rosenblum M, & Malkowski MG (2013). The Crystal Structure of α-Dioxygenase Provides Insight into Diversity in the Cyclooxygenase-Peroxidase Superfamily.
Biochemistry 52 :1364-1372.
PubMed Id: 23373518.
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doi: 10.1021/bi400013k.
Lipoxygenases
Related to Cyclooxygenases
Rather than being tethered by α-helices at the interface, they are tethered by N-terminal β-sheet C2-like domains
Arachidonic acid 15-lipoxygenase from soybeans: Glycine max  E Eukaryota, 2.60 Å
Boyington et al. (1993).
Boyington JC, Gaffney BJ, & Amzel LM (1993). The three-dimensional structure of an arachidonic acid 15-lipoxygenase.
Science 260 5113:1482-1486.
PubMed Id: 8502991.
doi: 10.1126/science.8502991.
Lipoxygenase-L1 from soybeans: Glycine max  E Eukaryota, 1.40 Å
Minor et al. (1996).
Minor W, Steczko J, Stec B, Otwinowski Z, Bolin JT, Walter R, & Axelrod B (1996). Crystal structure of soybean lipoxygenase L-1 at 1.4 A resolution.
Biochemistry 35 33:10687-10701.
PubMed Id: 8718858.
doi: 10.1021/bi960576u.
Lipoxygenase-L3 from soybeans: Glycine max  E Eukaryota, 2.60 Å
Skrzypczak-Jankun et al. (1997).
Skrzypczak-Jankun E, Amzel LM, Kroa BA, & Funk MO Jr (1997). Structure of soybean lipoxygenase L3 and a comparison with its L1 isoenzyme.
Proteins 29 1:15-31.
PubMed Id: 9294864.
doi: 10.1002/(SICI)1097-0134(199709)29:1.
8R-Lipoxygenase from coral: Plexaura homomalla  E Eukaryota (expressed in E. coli), 3.20 Å
2FNQ supersedes 1ZQ4
Oldham et al. (2005).
Oldham ML, Brash AR, & Newcomer ME (2005). Insights from the X-ray crystal structure of coral 8R-lipoxygenase: calcium activation via a C2-like domain and a structural basis of product chirality.
J Biol Chem 280 47:39545-39552.
PubMed Id: 16162493.
doi: 10.1074/jbc.M506675200.
8R-Lipoxygenase from coral. Δ413-417 I805A mutant: Plexaura homomalla  E Eukaryota (expressed in E. coli), 1.85 Å
Neau et al. (2009).
Neau DB, Gilbert NC, Bartlett SG, Boeglin W, Brash AR, & Newcomer ME (2009). The 1.85 A structure of an 8R-lipoxygenase suggests a general model for lipoxygenase product specificity.
Biochemistry 48 33:7906-7915.
PubMed Id: 19594169.
doi: 10.1021/bi900084m.
15-Lipoxygenase from rabbit reticulocytes: Oryctolagus cuniculus  E Eukaryota, 2.40 Å
Gillmor et al. (1997).
Gillmor SA, Villaseñor A, Fletterick R, Sigal E, & Browner MF (1997). The structure of mammalian 15-lipoxygenase reveals similarity to the lipases and the determinants of substrate specificity.
Nat Struct Mol Biol 4 12:1003-1009.
PubMed Id: 9406550.
doi: 10.1038/nsb1297-1003 .
5-Lipoxygenase: Homo sapiens  E Eukaryota (expressed in E. coli), 2.39 Å
Gilbert et al. (2011).
Gilbert NC, Bartlett SG, Waight MT, Neau DB, Boeglin WE, Brash AR, & Newcomer ME (2011). The structure of human 5-lipoxygenase.
Bensimon Marine Tennis Tennis Velvet Dots Velvet Velvet Marine Marine Tennis Dots Bensimon Bensimon Dots xvqzxfO Science 331 :217-219.
PubMed Id: 21233389.
doi: 10.1126/science.1197203.
15-Lipoxygenase-2 (15-LOX-2) with substrate mimic: Homo sapiens  E Eukaryota (expressed in E. coli), 2.63 Å
Kobe et al. (2014).
Kobe MJ, Neau DB, Mitchell CE, Bartlett SG, & Newcomer ME (2014). The structure of human 15-lipoxygenase-2 with a substrate mimic.
J Biol Chem 289 :8562-8569.
PubMed Id: 24497644.
doi: 10.1074/jbc.M113.543777.
Squalene-Hopene Cyclases
Squalene-hopene cyclase: Alicyclobacillus acidocaldarius  B Bacteria, 2.0 Å
2SQC is space group P4 32 12. 3SQC, 2.8 Å is P3 221.
Wendt et al. (1999).
Wendt KU, Lenhart A, & Schulz GE (1999). The structure of the membrane protein squalene-hopene cyclase at 2.0 Å resolution.
J. Mol. Biol. 286 :175-187.
PubMed Id: 9931258.
Oxidases
Monoamine Oxidase B: Homo sapiens (Human) mitochondrial outer membrane  E Eukaryota (expressed in Pichia pastoris), 3.0 Å
NOTE: MAOB has a single transmembrane helix that anchors it to the outer membrane (residues 489-515). Nevertheless, we consider it monotopic because the bulk of the 520-residue protein, including the active site, is not located within the membrane core.
Binda et al. (2002).
Binda C, Newton-Vinson P, Hubálek F, Edmondson DE, & Mattevi A (2002). Structure of human monoamine oxidase B, a drug target for the treatment of neurological disorders.
Nature Struct Biol 9 :22-26.
PubMed Id: 11753429.
Monoamine Oxidase B with bound Isatin: Homo sapiens (Human) mitochondrial outer membrane  E Eukaryota (expressed in Pichia pastoris), 1.70 Å
with bound Tranylcypromine, 2.20 Å: 1OJB
with bound N-(2-aminoethyl)- p-chlorobenamide, 2.40 Å: 1OJC
with bound Lauryldimethyl-amine N-Oxide, 3.10 Å: 1OJD
with bound 1.4-Diphenyl-2-butene, 2.30 Å: 1OJ9
Binda et al. (2003).
Binda C, Li M, Hubálek F, Restelli N, Edmondson DE, & Mattevi A (2003). Insights into the mode of inhibition of human mitochondrial monoamine oxidase B from high-resolution crystal structures.
Proc Natl Acad Sci USA 100 :9750-9755.
PubMed Id: 12913124.
Monoamine Oxidase A: Rattus norvegicus (Rat) mitochondrial outer membrane  E Eukaryota (expressed in S. cerevisiae), 3.20 Å
Ma et al. (2004).
Ma J, Yoshimura M, Yamashita E, Nakagawa A, Ito A, & Tsukihara T (2004). Structure of rat monoamine oxidase A and its specific recognitions for substrates and inhibitors.
J Mol Biol 338 :103-114.
PubMed Id: 15050826.
Monoamine Oxidase A with bound Clorglycine: Homo sapiens (Human) mitochondrial outer membrane  E Eukaryota (expressed in Pichia pastoris), 3.00 Å
crystal form B, 3.15 Å: 2BXS
Monoamine Oxidase B with bound Deprenyl, 2.20 Å: 2BYB
De Colibus et al. (2005).
De Colibus L, Li M, Binda C, Lustig A, Edmondson DE, & Mattevi A (2005). Three-dimensional structure of human monoamine oxidase A (MAO A): relation to the structures of rat MAO A and human MAO B.
Proc Natl Acad Sci USA 102 :12684-12689.
PubMed Id: 16129825.
Monoamine Oxidase A with bound Harmine: Homo sapiens (Human) mitochondrial outer membrane  E Eukaryota (expressed in S. cerevisiae), 2.20 Å
G110A mutant with bound Harmine, 2.17 Å: 2Z5Y
Son et al. (2008).
Son SY, Ma J, Kondou Y, Yoshimura M, Yamashita E, & Tsukihara T (2008). Structure of human monoamine oxidase A at 2.2-Å resolution: The control of opening the entry for substrates/inhibitors.
Proc Natl Acad Sci USA 105 :5739-5744.
PubMed Id: 18391214.
Alternative oxidase (AOX), cyanide-insensitive: Trypanosoma brucei brucei  E Eukaryota (expressed in E. coli), 2.85 Å
with ascofuranone derivative, 2.59 Å: 3VVA
with colletochlorin B, 2.30 Å: 3W54
Shiba et al. (2013).
Shiba T, Kido Y, Sakamoto K, Inaoka DK, Tsuge C, Tatsumi R, Takahashi G, Balogun EO, Nara T, Aoki T, Honma T, Tanaka A, Inoue M, Matsuoka S, Saimoto H, Moore AL, Harada S, & Kita K (2013). Structure of the trypanosome cyanide-insensitive alternative oxidase.
Proc Natl Acad Sci USA 110 :4580-4585.
PubMed Id: 23487766.
doi: 10.1073/pnas.1218386110.
Hydrolases
Fatty acid amide hydrolase: Rattus norvegicus  E Eukaryota, 2.8 Å
NOTE: Like MAO, FAAH has a single TM segment. But the active site is external to the membrane, and many other residues on the protein surface contribute to membrane binding. Absence of the TM segment affects neither membrane association or function.
Bracey et al. (2002).
Bracey MH, Hanson MA, Masuda KR, Stevens RC, & Cravatt BF (2002). Structural adaptations in a membrane enzyme that terminates endo cannabinoid signaling.
Science 298 :1793-1796.
PubMed Id: 12459591.
LpxH pyrophosphohydrase with bound lipid X & Mn2+: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), 1.65 Å
complex with lipid X, P21 form, 1.72 Å: 5B4A
complex with lipid X, C2 form, 1.6 Å: 5B4B
H10N mutant in complex with Mn 2+, 1.96 Å: 5B4C
H10N mutant, 1.75 Å: 5B4D
Okada et al. (2016).
Okada C, Wakabayashi H, Kobayashi M, Shinoda A, Tanaka I, & Yao M (2016). Crystal structures of the UDP-diacylglucosamine pyrophosphohydrase LpxH from Pseudomonas aeruginosa.
Sci Rep 6 :32822.
PubMed Id: 27609419.
doi: 10.1038/srep32822.
LpxI phosphodiester hydrolase for lipid A biosynthesis: Caulobacter crescentus  B Bacteria (expressed in E. coli), 2.90 Å
D225A mutant, 2.52 Å: 4GGI
Metzger et al. (2012).
Metzger LE 4th, Lee JK, Finer-Moore JS, Raetz CR, & Stroud RM (2012). LpxI structures reveal how a lipid A precursor is synthesized.
Nature Struc Mol Biol 19 :1132-1138.
PubMed Id: 23042606.
doi: 10.1038/nsmb.2393.
LpxK, the 4'-kinase of lipid A biosynthesis: Aquifex aeolicus  B Bacteria (expressed in E. coli), 2.30 Å
Apo LpxK, 1.90 Å: 4EHX
ADP/Mg 2+ LpxK, 2.20 Å: 4EHY
Emptage et al. (2012).
Emptage RP, Daughtry KD, Pemble CW 4th, & Raetz CR (2012). Crystal structure of LpxK, the 4'-kinase of lipid A biosynthesis and atypical P-loop kinase functioning at the membrane interface.
Proc Natl Acad Sci USA 109 :12956-12961.
PubMed Id: 22826246.
doi: 10.1073/pnas.1206072109.
N-acylphosphatidylethanolamine-hydrolyzing phospholipase D: Homo sapiens  E Eukaryota (expressed in Buscemi Uno 5 Box Sneakers White New Low Out Alce In Sneakers 39 Sold E. coli), 2.65 Å
Magotti et al. (2015).
Magotti P, Bauer I, Igarashi M, Babagoli M, Marotta R, Piomelli D, & Garau G (2015). Structure of human N-acylphosphatidylethanolamine-hydrolyzing phospholipase D: regulation of Fatty Acid ethanolamide biosynthesis by bile acids.
Structure 23 3:598-604.
PubMed Id: 25684574.
doi: 10.1016/j.str.2014.12.018.
PulA pullulanase: Klebsiella oxytoca  B Bacteria (expressed in E. coli), 2.88 Å
East et al. (2016).
East A, Mechaly AE, Huysmans GH, Bernarde C, Tello-Manigne D, Nadeau N, Pugsley AP, Buschiazzo A, Alzari PM, Bond PJ, & Francetic O (2016). Structural Basis of Pullulanase Membrane Binding and Secretion Revealed by X-Ray Crystallography, Molecular Dynamics and Biochemical Analysis.
Structure 24 :92-104.
PubMed Id: 26688215.
doi: 10.1016/j.str.2015.10.023.
Acyltransferases
LpxM lipid A acyltransferase: Acinetobacter baumannii  B Bacteria (expressed in E. coli), 1.99 Å
The protein is anchored at the membrane interface by a single TM helix.
E127A catalytic residue mutant, 1.9 Å: 5KNK
Dovala et al. (2016).
Dovala D, Rath CM, Hu Q, Sawyer WS, Shia S, Elling RA, Knapp MS, & Metzger LE 4th (2016). Structure-guided enzymology of the lipid A acyltransferase LpxM reveals a dual activity mechanism.
Proc Natl Acad Sci USA 113 :E6064-E6071.
PubMed Id: 27681620.
doi: 10.1073/pnas.1610746113.
Oxidoreductases (Monotopic)
Sulfide:quinone oxidoreductase in complex with decylubiquinone: Aquifex aeolicus  B Bacteria, 2.0 Å
"as-purified" protein, 2.30 Å: 3HYV
in complex with aurachin C, 2.9 Å: 3HYX
This monotopic membrane protein is thought to be buried about 12 Å in the bilayer interface.
Listed under TRANSMEMBRANE PROTEINS: ALPHA-HELICAL : Oxidoreductases, MONOTOPIC MEMBRANE PROTEINS : Oxidoreductases (Monotopic).
Marcia et al. (2009).
Marcia M, Ermler U, Peng G, & Michel H (2009). The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration.
Proc Natl Acad Sci USA 106 :9625-9630.
PubMed Id: 19487671.
Electron Transfer Flavoprotein-ubiquinone oxidoreductase (ETF-QO) with bound UQ: Sus scrofa  E Eukaryota, 2.5 Å
UQ-free structure, 2.6 Å: 2GMJ.
Because this is a mitochondrial respiratory chain protein, it is listed under TRANSMEMBRANE PROTEINS: ALPHA-HELICAL : Oxidoreductases and MONOTOPIC MEMBRANE PROTEINS : Oxidoreductases (Monotopic).
Zhang et al. (2006).
Zhang J, Frerman FE, & Kim J-JP (2006). Structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool.
Proc Natl Acad Sci U S A 103 :16212-16217.
PubMed Id: 17050691.
Dehydrogenases
Glycerol-3-phosphate dehydrogenase (GlpD, native): Escherichia coli  B Bacteria, 1.75 Å
SeMet-GlpD, 1.95 Å: 2R4J
GlpD-2-PGA, 2.3 Å: 2R45
GlpD-PEP, 2.1 Å: 2R46
GlpD-DHAP, 2.1 Å: 2R4E
Listed under MONOTOPIC MEMBRANE PROTEINS : Dehydrogenases, TRANSMEMBRANE PROTEINS: ALPHA-HELICAL : Oxidoreductases.
Yeh et al. (2008).
Yeh JI, Chinte U, & Du S (2008). Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism.
Proc. Natl. Acad. Sci. USA 105 :3280-3285.
PubMed Id: 18296637.
PutA proline utilization protein: Geobacter sulfurreducens  B Bacteria (expressed in E. coli), 1.90 Å
in complex with L-tetrahydro-2-furoic acid, 2.10 Å: 4NMA
in complex with L-lactate, 2.2 Å: 4NMB
in complex with Zwittergent 3-12, 1.90 Å: 4NMC
reduced with dithionite, 1.98 Å: 4NMD
inactivated by N-propargylglycine, 2.09 Å: 4NME
inactivated by N-propargylglycine and complexed with menadione bisulfite, 1.95 Å: 4NMF
Singh et al. (2014).
Singh H, Arentson BW, Becker DF, & Tanner JJ (2014). Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site.
Proc Natl Acad Sci USA 111 :3389-3394.
PubMed Id: 24550478.
doi: 10.1073/pnas.1321621111.
Ndi1 NADH Dehydrogenase: Saccharomyces cerevisiae  E Eukaryota, 2.70 Å
Ndi1-NAD + complex, 2.90 Å: 4GAP
Ndi1-UQ2 complex, 3.00 Å: 4GAV
Iwata et al. (2012).
Iwata M, Lee Y, Yamashita T, Yagi T, Iwata S, Cameron AD, & Maher MJ (2012). The structure of the yeast NADH dehydrogenase (Ndi1) reveals overlapping binding sites for water- and lipid-soluble substrates.
Proc Natl Acad Sci USA 109 :15247-15252.
PubMed Id: 22949654.
doi: 10.1073/pnas.1210059109 .
Ndi1 NADH Dehydrogenase, apo form: Saccharomyces cerevisiae  E Eukaryota (expressed in E. coli), 2.39 Å
with NADH, 2.26 Å: 4G6H
with Quinone, 2.48 Å: 4G74
with NAH and Quinone, 2.52 Å: 4G73
Feng et al. (2012).
Feng Y, Li W, Li J, Wang J, Ge J, Xu D, Liu Y, Wu K, Zeng Q, Wu JW, Tian C, Zhou B, & Yang M (2012). Structural insight into the type-II mitochondrial NADH dehydrogenases.
Nature 491 :478-482.
PubMed Id: 23086143.
doi: 10.1038/nature11541.
NDH-2 NADH dehydrogenase: Caldalkalibacillus thermarum  B Bacteria (expressed in E. coli), 2.50 Å
NDH-2 is a non-proton pumping dehydrogenase.
Heikal et al. (2014).
Heikal A, Nakatani Y, Dunn E, Weimar MR, Day CL, Baker EN, Lott JS, Sazanov LA, & Cook GM (2014). Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation.
Mol Microbiol 91 5:950-964.
PubMed Id: 24444429.
doi: 10.1111/mmi.12507.
Glycosyltransferases
Peptidoglycan Glycosyltransferase: Staphylococcus aureus  B Bacteria, 2.8 Å
NOTE: The enzyme has a single TM segment, which is absent in the structure. The active site is external to the membrane, but the so-called Jaw Region contributes to membrane binding. 2OLV shows the enzyme complexed with moenomycin. 2OLU is the structure of the apoenzyme.
Lovering et al. (2007).
Lovering AL, de Castro LH, Lim D, & Strynadka NCJ (2007). Structural insight into the transglycosylation step in bacterial cell-wall biosynthesis.
Science 315 :1402-1405.
PubMed Id: 17347437.
Peptidoglycan Glycosyltransferase penicillin-binding protein 1a (PBP1a): Aquifex aeolicus  B Bacteria (expressed in E. coli), 2.1 Å
NOTE: The enzyme has a single TM segment, which is absent in the structure. The active site is external to the membrane.
Yuan et al. (2007).
Yuan Y, Barrett D, Zhang Y, Kahne D, Sliz P, & Walker S. (2007). Crystal structure of a peptidoglycan glycosyltransferase suggests a model for processive glycan chain synthesis.
Proc Natl Acad Sci USA 104 :5348-5353.
PubMed Id: 17360321.
Peptidoglycan Glycosyltransferase penicillin-binding protein 1b (PBP1b): Escherichia coli  B Bacteria, 2.16 Å
3VMA supersedes the original PDB entry 3FWM.
NOTE: The single TM segment is present in this structure. The active site is external to the membrane.
SeMet Protein, 3.09 Å: 3FWL
Sung et al. (2009).
Sung MT, Lai YT, Huang CY, Chou LY, Shih HW, Cheng WC, Wong CH, & Ma C (2009). Crystal structure of the membrane-bound bifunctional transglycosylase PBP1b from Escherichia coli.
Proc Natl Acad Sci USA 106 :8824-8829.
PubMed Id: 19458048.
Monofunctional glycosyltransferase WaaA, substrate free: Aquifex aeolicus  B Bacteria (expressed in E. coli), 2.00 Å
WaaA catalyzes the transfer of Kdo to the lipid A precursor of lipopolysaccharide.
Structure with substrate, 2.42 Å: 2XCU
Schmidt et al. (2012).
Schmidt H, Hansen G, Singh S, Hanuszkiewicz A, Lindner B, Fukase K, Woodard RW, Holst O, Hilgenfeld R, Mamat U, & Mesters JR (2012). Structural and mechanistic analysis of the membrane-embedded glycosyltransferase WaaA required for lipopolysaccharide synthesis.
Proc Natl Acad Sci USA 109 :6253-6258.
PubMed Id: 22474366.
doi: 10.1073/pnas.1119894109.
Monofunctional glycosyltransferase in complex with Lipid II analog: Staphylococcus aureus  B Bacteria (expressed in E. coli), 2.30 Å
NOTE: The single TM segment is present in this structure. The active site is external to the membrane.
Substrate-free protein, 2.52 Å: 3VMQ
In complex with moenomycin, 3.69 Å: 3VMR
In complex with NBD-Lipid II, 3.20 Å: 3VMS
Huang et al. (2012).
Huang CY, Shih HW, Lin LY, Tien YW, Cheng TJ, Cheng WC, Wong CH, & Ma C (2012). Crystal structure of Staphylococcus aureus transglycosylase in complex with a lipid II analog and elucidation of peptidoglycan synthesis mechanism.
Proc Natl Acad Sci USA 109 :6496-6501.
PubMed Id: 22493270.
doi: 10.1073/pnas.1203900109.
PglH glycosyltransferase in complex with UDP-galNAc: Campylobacter jejuni  B Bacteria (expressed in E. coli), 2.3 Å
in complex w. UDP & synthetic LLO, 2.7 Å: 6EJJ
in complex with UDP-CH 2-GalNAc, 3.3 Å: 6EJK
Ramírez et al. (2018).
Ramírez AS, Boilevin J, Mehdipour AR, Hummer G, Darbre T, Reymond JL, & Locher KP (2018). Structural basis of the molecular ruler mechanism of a bacterial glycosyltransferase.
Nat Commun 9 1:445.
PubMed Id: 29386647.
doi: 10.1038/s41467-018-02880-2.
Phosphoglycosyl Transferases (PGT)
These proteins catalyze the first membrane-committed step of glycoconjugates
PglC phosphoglycosyl transferase, I57M/Q175M variant: Campylobacter concisus  B Bacteria (expressed in E. coli), 2.74 Å
Ray et al. (2018).
Ray LC, Das D, Entova S, Lukose V, Lynch AJ, Imperiali B, & Allen KN (2018). Membrane association of monotopic phosphoglycosyl transferase underpins function.
Nat Chem Biol 14 :538-541.
PubMed Id: 29769739.
doi: 10.1038/s41589-018-0054-z.
Peptidases
LepB Signal Peptidase (SPase) in complex with a β-lactam inhibitor: Escherichia coli  B Bacteria, 1.9 Å
Located in the periplasmic space, the SPase has two transmembrane segments (AAs 4-28 & 58-76), which are missing in this structure. The Ser-Lys catalytic site is part of a hydrophobic surface that interacts strongly with the membrane.
Paetzel et al. (1998).
Paetzel M, Dalbey RE, & Strynadka NC (1998). Crystal structure of a bacterial signal peptidase in complex with a β-lactam inhibitor.
Nature 396 :186-190.
PubMed Id: 9823901.
LepB Signal Peptidase (SPase), apoprotein: Escherichia coli  B Bacteria, 2.40 Å
Δ2-75 protein lacking the two transmembrane helices
Paetzel et al. (2002).
Paetzel M, Dalbey RE, & Strynadka NC (2002). Crystal structure of a bacterial signal peptidase apoenzyme
J Biol Chem 277 :9512-9519.
PubMed Id: 11741964.
LepB Signal Peptidase (SPase) in complex with a lipopeptide inhibitor: Escherichia coli  B Bacteria, 2.47 Å
This structure of the Δ2-75 protein reveals the likely position of the signal peptide in the active site.
Paetzel et al. (2004).
Paetzel M, Goodall JJ, Kania M, Dalbey RE, & Page MG (2004). Crystallographic and biophysical analysis of a bacterial signal peptidase in complex with a lipopeptide-based inhibitor.
J Biol Chem 279 :30781-30790.
PubMed Id: 15136583.
SpsB Signal Peptidase (SPase), apoprotein: Staphylococcus aureus  B Bacteria (expressed in E. coli), 2.05 Å
in complex with peptide 1, 2.10 Å: 4WVH
in complex with peptide 2, 1.90 Å: 4WVI
in complex with peptide 3, 1.95 Å: 4WVJ
Ting et al. (2015).
Ting YT, Batot G, Baker EN, & Young PG (2015). Expression, purification and crystallization of a membrane-associated, catalytically active type I signal peptidase from Staphylococcus aureus.
Acta Crystallogr F Struct Biol Commun 71 :61-65.
PubMed Id: 25615971.
doi: 10.1107/S2053230X1402603X.
Signal Peptide Peptidase (SppA), native protein: Escherichia coli  B Bacteria, 2.55 Å
SeMet protein, 2.76 Å: 3BEZ.
Long thought to be a transmembrane protein, the structure reveals a peripheral homotetramer that likely is buried in the membrane interface. Each monomer has a putative N-terminal transmembrane helix for anchoring to the membrane. This anchor was removed for crystallization.
Listed under TRANSMEMBRANE PROTEINS: ALPHA-HELICAL : Intramembrane Proteases, MONOTOPIC MEMBRANE PROTEINS : Peptidases.
Kim et al. (2008).
Kim AC, Oliver DC, & Paetzel M (2008). Crystal structure of a bacterial signal Peptide peptidase.
J Mol Biol 376 :352-366.
PubMed Id: 18164727.
Signal Peptide Peptidase (SppA): Bacillus subtilis  B Bacteria (expressed in E. coli), 2.37 Å
Each monomer of the homooctamer has a putative N-terminal transmembrane helix for anchoring to the membrane. This anchor was removed for crystallization.
Listed under TRANSMEMBRANE PROTEINS: ALPHA-HELICAL : Intramembrane Proteases, MONOTOPIC MEMBRANE PROTEINS : Peptidases.
Nam et al. (2012).
Nam SE, Kim AC, & Paetzel M (2012). Crystal Structure of Bacillus subtilis Signal Peptide Peptidase A.
J Mol Biol 419 :347-358.
PubMed Id: 22472423.
doi: 10.1016/j.jmb.2012.03.020.
Signal Peptide Peptidase (SppA) K199A mutant showing C-terminal peptide bound in eight active sites: Bacillus subtilis  B Bacteria (expressed in E. coli), 2.39 Å
Each monomer of the homooctamer has a putative N-terminal transmembrane helix for anchoring to the membrane. This anchor was removed for crystallization.
Listed under TRANSMEMBRANE PROTEINS: ALPHA-HELICAL : Intramembrane Proteases, MONOTOPIC MEMBRANE PROTEINS : Peptidases.
Nam & Paetzel (2013).
Nam SE, & Paetzel M (2013). Structure of Signal Peptide Peptidase A with C-Termini Bound in the Active Sites: Insights into Specificity, Self-Processing, and Regulation.
Biochemistry 52 :8811-8822.
PubMed Id: 24228759.
Meprin β sheddase (metalloproteinase), pro-form: Homo sapiens  E Eukaryota (expressed in Trichoplusia ni), 1.85 Å
Mature form, 3.00 Å: 4GWN
Arolas et al. (2012).
Arolas JL, Broder C, Jefferson T, Guevara T, Sterchi EE, Bode W, Stöcker W, Becker-Pauly C, & Gomis-Rüth FX (2012). Structural basis for the sheddase function of human meprin β metalloproteinase at the plasma membrane.
Proc Natl Acad Sci USA 109 :16131-16136.
PubMed Id: 22988105.
doi: 10.1073/pnas.1211076109.
Cytochromes P450
P450s are members of the CYP51 family involved in sterol biosynthesis
Lanosterol 14α-demethylase with bound lanosterol: Saccharomyces cerevisiae  E Eukaryota, 1.90 Å
with bound itraconazole, 2.19 Å: 5EQB. Supersedes 4K0F.
This is the first structure of a full-length single-span 'bitopic' membrane protein. Proteins of this structural type are anchored at the membrane surface by one or two TM segments, which are generally not seen in the structures. See, for example, 1B12.
Monk et al. (2014).
Monk BC, Tomasiak TM, Keniya MV, Huschmann FU, Tyndall JD, O'Connell JD 3rd, Cannon RD, McDonald JG, Rodriguez A, Finer-Moore JS, & Stroud RM (2014). Architecture of a single membrane spanning cytochrome P450 suggests constraints that orient the catalytic domain relative to a bilayer.
Proc Natl Acad Sci USA 111 :3865-3870.
PubMed Id: 24613931.
doi: 10.1073/pnas.1324245111.
Dihydroorotate Dehydrogenases (DHODH, class 2)
Class 1 DHODHs are soluble proteins. Class 2 are membrane associated proteins.
Dihydroorotate Dehydrogenase: Escherichia coli  B Bacteria, 1.70 Å
Thoden et al. (2001).
Thoden JB, Phillips GN Jr, Neal TM, Raushel FM, & Holden HM (2001). Molecular structure of dihydroorotase: a paradigm for catalysis through the use of a binuclear metal center.
Biochemistry 40 :6989-6997.
PubMed Id: 11401542.
Dihydroorotate Dehydrogenase: Escherichia coli  B Bacteria, 1.90 Å
Lee et al. (2005).
Lee M, Chan CW, Mitchell Guss J, Christopherson RI, & Maher MJ (2005). Dihydroorotase from Escherichia coli: loop movement and cooperativity between subunits.
J Mol Biol 348 :523-533.
PubMed Id: 15826651.
Dihydroorotate Dehydrogenase in complex with atovaquone: Rattus rattus  E Eukaryota (expressed in E. coli), 2.30 Å
DHO in complex with brequinar, 2.40 Å: 1UUO
Hansen et al. (2004).
Hansen M, Le Nours J, Johansson E, Antal T, Ullrich A, Löffler M, & Larsen S (2004). Inhibitor binding in a class 2 dihydroorotate dehydrogenase causes variations in the membrane-associated N-terminal domain.
Protein Sci 13 :1031-1042.
PubMed Id: 15044733.
Dihydroorotate Dehydrogenase, apo form: Homo sapiens  E Eukaryota (expressed in E. coli), 3.00 Å
DHODH in complex with brequinar analogue, 2.40 Å: 2PRH
DHODH in complex with 'a novel inhibitor', 3.00 Å: 2PRL
Walse et al. (2008).
Walse B, Dufe VT, Svensson B, Fritzson I, Dahlberg L, Khairoullina A, Wellmar U, & Al-Karadaghi S (2008). The structures of human dihydroorotate dehydrogenase with and without inhibitor reveal conformational flexibility in the inhibitor and substrate binding sites.
Biochemistry 47 :8929-8936.
PubMed Id: 18672895.
Dihydroorotate Dehydrogenase with triazolopyrimidine-based inhibitor DSM1: Plasmodium falciparum 3d7  E Eukaryota (expressed in E. coli), 2.00 Å
With bound triazolopyrimidine-based inhibitor DSM2, 2.40 Å: 3I68
With bound triazolopyrimidine-based inhibitor DSM74, 2.50 Å: 3I6R
Deng et al. (2009).
Deng X, Gujjar R, El Mazouni F, Kaminsky W, Malmquist NA, Goldsmith EJ, Rathod PK, & Phillips MA (2009). Structural plasticity of malaria dihydroorotate dehydrogenase allows selective binding of diverse chemical scaffolds.
J Biol Chem 284 :26999-27009.
PubMed Id: 19640844.
Polymerases
TagF teichoic acid polymerase: Staphylococcus epidermidis  B Bacteria (expressed in E. coli), 2.70 Å
H444N mutant, 2.81 Å: 3L7J
H444N + CDPG, 15' soak, 3.10 Å: 3L7K
H444N + CDPG, 30' soak, 2.95 Å: 3L7L
H584A mutant, 2.85 Å: 3L7M
Lovering et al. (2010).
Lovering AL, Lin LY, Sewell EW, Spreter T, Brown ED, & Strynadka NC (2010). Structure of the bacterial teichoic acid polymerase TagF provides insights into membrane association and catalysis.
Nat Struct Mol Biol Box Out 5 In Low Buscemi Sneakers Uno New Sold Sneakers Alce 39 White 17 :582-589.
PubMed Id: 20400947.
ADP-Ribosylation Factors
ADP-ribosylation factor (ARF1), myristoylated: Saccharomyces cerevisiae  E Eukaryota (expressed in E. coli), NMR Structure
Liu et al. (2009).
Liu Y, Kahn RA, & Prestegard JH (2009). Structure and Membrane Interaction of Myristoylated ARF1.
Structure 17 :79-87.
PubMed Id: 19141284.
ADP-ribosylation factor (ARF1*GTP), myristoylated: Saccharomyces cerevisiae  E Eukaryota (expressed in E. coli), NMR Structure
Liu et al. (2010).
Liu Y, Kahn RA, & Prestegard JH (2010). Dynamic structure of membrane-anchored Arf*GTP.
Nature Struct Molec Biol 17 :876-881.
PubMed Id: 20601958.
Isomerases
RPE65 visual cycle retinoid isomerase: Bos taurus  E Eukaryota, 2.14 Å
This retinal pigment epithelium (RPE) protein simultaneously cleaves and isomerizes all- trans-retinyl esters to 11- cis-retinol and a fatty acid.
Kiser et al. (2009).
Kiser PD, Golczak M, Lodowski DT, Chance MR, Palczewski K (2009). Crystal structure of native RPE65, the retinoid isomerase of the visual cycle.
Proc Natl Acad Sci USA 106 :17325-17330.
PubMed Id: 19805034.
RPE65 visual cycle retinoid isomerase in a lipid matrix (crystal form C): Bos taurus  E Eukaryota, 2.50 Å
Crystal form A, 3.00 Å: 4F2Z
Crystal form B, iridium derivative, 2.60 Å: 4F3A
Crystal form B, native, 3.15 Å: 4F30
Kiser In Low Box Sold Alce 5 Sneakers Out Buscemi Sneakers 39 New Uno White et al. (2012).
Kiser PD, Farquhar ER, Shi W, Sui X, Chance MR, & Palczewski K (2012). Structure of RPE65 isomerase in a lipidic matrix reveals roles for phospholipids and iron in catalysis.
Proc Natl Acad Sci USA 109 :E2747-2756.
PubMed Id: 23012475.
Phosphoinositide Kinases
Phosphatidylinositol 4-kinase IIα: Homo sapiens  E Eukaryota (expressed in E. coli), 2.77 Å
Baumlova et al. (2014).
Baumlova A, Chalupska D, Róźycki B, Jovic M, Wisniewski E, Klima M, Dubankova A, Kloer DP, Nencka R, Balla T, & Boura E (2014). The crystal structure of the phosphatidylinositol 4-kinase II?.
EMBO Rep 15 :1085-1092.
PubMed Id: 25168678.
doi: 10.15252/embr.201438841.
TRANSMEMBRANE PROTEINS: BETA-BARREL
Beta-Barrel Membrane Proteins: Porins and Relatives
Porin: Rhodobacter capsulatus  B Bacteria, 1.8 Å
Weiss & Schulz (1992).
Weiss MS & Schulz GE (1992). Structure of porin refined at 1.8 Å resolution.
J. Mol. Biol. 227 :493-509.
PubMed Id: 1328651.
Porin: Rhodopeudomonas blastica  B Bacteria, 1.96 Å
Kreusch & Schulz (1994).
Kreusch A & Schulz GE (1994). Refined structure of the porin from Rhodopseudomonas blastica. Comparison with the porin from Rhodobacter capsulatus.
J Mol Biol 243 :891-905.
PubMed Id: 7525973.
doi: 10.1006/jmbi.1994.1690.


See also:
Kreusch et al. (1994).
Kreusch A, Neubüser A, Schiltz E, Weckesser J, & Schulz GE (1994). Structure of the membrane channel porin from Rhodopseudomonas blastica at 2.0 Å resolution.
Protein Sci 3 :58-63.
PubMed Id: 8142898.
doi: 10.1002/pro.5560030108.
Porin, E1M/A116K Mutant: Rhodopseudomonas blastica  B Bacteria (expressed in E. coli), 2.19 Å
E1M/E99W/A116W mutant, 1.93 Å: 2PRN
E1M/A104W mutant, 1.90 Å: 3PRN
E1M/Y96W/S119W mutant, 2.00 Å: 5PRN
E1M/K50A/R52A mutant, 2.04 Å: 6PRN
E1M/D97A/E99A mutant, 2.25 Å: 7PRN
E1M/K50A/R52A/D97A/E99A mutant, 2.30 Å: 8PRN
Schmid et al. (1998).
Schmid B, Maveyraud L, Krömer M, & Schulz GE (1998). Porin mutants with new channel properties.
Protein Sci 7 :1603-1611.
PubMed Id: 9684893.
doi: 10.1002/pro.5560070714.
Porin: Rhodopseudomonas blastica  B Bacteria (expressed in E. coli), 3.00 Å
Positively charged peptide GGGGPKLAKMEKARGGGG inserted in periplasmic turn.
Bannwarth & Schulz (2002).
Bannwarth M & Schulz GE (2002). Asymmetric conductivity of engineered porins.
Protein Eng 15 :799-804.
PubMed Id: 12468713.
doi: 10.1093/protein/15.10.799.
OmpK36 osmoporin: Klebsiella pneumoniae  B Bacteria, 3.2 Å
Dutzler et al. (1999).
Dutzler R, Rummel G, Alberti S, Hernandez-Alles S, Phale P, Rosenbusch J, Benedi V, & Schirmer T (1999). Crystal structure and functional characterization of OmpK36, the osmoporin of Klebsiella pneumoniae.
Structure Fold. Des 7 :425-434.
PubMed Id: 10196126.
Omp32 anion-selective porin: Comamonas acidovorans  B Bacteria, 2.1 Å
Zeth et al. (2000).
Zeth K, Diederichs K, Welte W, & Engelhardt H (2000). Crystal structure of Omp32, the anion-selective porin from Comamonas acidovorans, in complex with a periplasmic peptide at 2.1 A resolution.
Structure 8 :981-992.
PubMed Id: 10986465.
Omp32 anion-selective porin: Delftia acidovorans  B Bacteria, 1.5 Å
With bound malate, 1.45 Å: 2FGQ
Zachariae et al. (2006).
Zachariae U, Kluhspies T, De S, Engelhardt H, & Zeth K (2006). High resolution crystal structures and molecular dynamics studies reveal substrate binding in the porin omp32.
J Biol Chem 281 :7413-7420.
PubMed Id: 16434398.
OmpF Porin: Escherichia coli  B Bacteria, 2.4 Å
Note: Also see BtuB with bound colicin E3 R-domain, below.
Cowan et al. (1992).
Cowan SW, Schirmer T, Rummel G, Steiert M, Ghosh R, Pauptit RA, Jansonius JN, & Rosenbusch JP (1992). Crystal structures explain functional properties of two Escherichia coli porins.
Nature 358 :727-733.
PubMed Id: 1380671.
OmpF Porin from colicin-resistant E. coli: Escherichia coli  B Bacteria, 3.00 Å
Jeanteur et al. (1994).
Jeanteur D, Schirmer T, Fourel D, Simonet V, Rummel G, Widmer C, Rosenbusch JP, Pattus F, & Pagès JM (1994). Structural and functional alterations of a colicin-resistant mutant of OmpF porin from Escherichia coli.
Proc Natl Acad Sci USA 91 :10675-10679.
PubMed Id: 7524100.
OmpF Porin: Escherichia coli  B Bacteria, 3.20 Å
Tetragonal crystal form.
Cowan et al. (1995).
Cowan SW, Garavito RM, Jansonius JN, Jenkins JA, Karlsson R, König N, Pai EF, Pauptit RA, Rizkallah PJ, Rosenbusch JP, Rummel G, & Schirmer T (1995). The structure of OmpF porin in a tetragonal crystal form.
Structure 3 :1041-1050.
PubMed Id: 8589999.
doi: 10.1016/S0969-2126(01)00240-4.
OmpF Porin, D113G mutant: Escherichia coli  B Bacteria, 3.50 Å
Deletion Mutant (Δ 109-114), 3.10 Å: 1GFN
R132P Mutant, 3.30 Å: 1GFO
R42C Mutant, 2.70 Å: 1GFP
R82C Mutant, 2.80 Å: 1GFQ
Lou et al. (1996).
Lou KL, Saint N, Prilipov A, Rummel G, Benson SA, Rosenbusch JP, & Schirmer T (1996). Structural and functional characterization of OmpF porin mutants selected for larger pore size. I. Crystallographic analysis.
J Biol Chem 271 :20669-20675.
PubMed Id: 8702816.
doi: 10.1074/jbc.271.34.20669 .
OmpF Porin, D74A mutant: Escherichia coli  B Bacteria (expressed in Escherichia coli B), 3.00 Å
Phale et al. (1998).
Phale PS, Philippsen A, Kiefhaber T, Koebnik R, Phale VP, Schirmer T, & Rosenbusch JP (1998). Stability of trimeric OmpF porin: the contributions of the latching loop L2.
Biochemistry 37 :15663-15670.
PubMed Id: 9843370.
doi: 10.1021/bi981215c.
OmpF Porin, Y106F Mutant: Escherichia coli  B Bacteria, 2.20 Å
NQAAA (D113N/E117Q/R42A/R82A/R132A) Mutant, 2.40 Å: 1HXT
KK (V18K/G131K) Mutant, 3.00 Å: 1HXU
Phale et al. (2001).
Phale PS, Philippsen A, Widmer C, Phale VP, Rosenbusch JP, & Schirmer T (2001). Role of charged residues at the OmpF porin channel constriction probed by mutagenesis and simulation.
Biochemistry 40 :6319-6325.
PubMed Id: 11371193.
doi: 10.1021/bi010046k.
OmpF Porin: Escherichia coli  B Bacteria, 1.6 Å
With inserted 83 residue N-terminal peptide of colicin E3, 3.0 Å: 2ZLD
Yamashita et al. (2008).
Yamashita E, Zhalnina MV, Zakharov SD, Sharma O, & Cramer WA (2008). Crystal structures of the OmpF porin: function in a colicin translocon.
EMBO J 27 :2171-2180.
PubMed Id: 18636093.
OmpF porin with a synthetic dibenzo-18-crown-6: Escherichia coli  B Bacteria, 3.40 Å
Reitz et al. (2009).
Reitz S, Cebi M, Reiss P, Studnik G, Linne U, Koert U, & Essen LO (2009). On the function and structure of synthetically modified porins.
Angew Chem Int Ed Engl 48 :4853-4857.
PubMed Id: 19322865.
doi: 10.1002/anie.200900457.
OmpF Porin in complex with colicin peptide OBS1: Escherichia coli  B Bacteria, 3.01 Å
Shows colicin bound within porin lumen spanning the membrane bilayer
Housden et al. (2010).
Housden NG, Wojdyla JA, Korczynska J, Grishkovskaya I, Kirkpatrick N, Brzozowski AM, & Kleanthous C. (2010). Directed epitope delivery across the Escherichia coli outer membrane through the porin OmpF.
Proc Natl Acad Sci USA 107 :21412-21417.
PubMed Id: 21098297.
OmpF Porin: Escherichia coli  B Bacteria, 2.61 Å
Cation-selective pathway revealed by anomalous x-ray diffraction.
Structure at 3.00 Å: 3HWB
Dhakshnamoorthy et al. (2010).
Dhakshnamoorthy B, Raychaudhury S, Blachowicz L, & Roux B (2010). Cation-selective pathway of OmpF porin revealed by anomalous X-ray diffraction.
J Mol Biol 396 :293-300.
PubMed Id: 19932117.
doi: 10.1016/j.jmb.2009.11.042.
OmpF Porin in presence of foscholine-12: Escherichia coli  B Bacteria, 3.79 Å
Structure at 4.39 Å: 3K1B
Kefala et al. (2010).
Kefala G, Ahn C, Krupa M, Esquivies L, Maslennikov I, Kwiatkowski W, & Choe S (2010). Structures of the OmpF porin crystallized in the presence of foscholine-12.
Protein Sci 19 :1117-1125.
PubMed Id: 20196071.
doi: 10.1002/pro.369.
OmpF Porin: Escherichia coli  B Bacteria, 3.5 Å
I2 space group
Chaptal et al. (2016).
Chaptal V, Kilburg A, Flot D, Wiseman B, Aghajari N, Jault JM, & Falson P (2016). Two different centered monoclinic crystals of the E. coli outer-membrane protein OmpF originate from the same building block.
Biochim Biophy Acta 1858 :326-332.
PubMed Id: 26620074.
doi: 10.1016/j.bbamem.2015.11.021.
OmpF Porin: Salmonella typhi  B Bacteria (expressed in E. coli), 2.79 Å
Balasubramaniam et al. (2012).
Balasubramaniam D, Arockiasamy A, Kumar PD, Sharma A, & Krishnaswamy S (2012). Asymmetric pore occupancy in crystal structure of OmpF porin from Salmonella typhi.
J Struc Biol 178 :233-244.
PubMed Id: 22525817.
doi: 10.1016/j.jsb.2012.04.005.
OmpC Osmoporin: Escherichia coli  B Bacteria, 2.0 Å
Baslé et al. (2006).
Baslé A, Rummel G, Storici P, Rosenbusch J, & Schirmer T (2006). Crystal Structure of Osmoporin OmpC from E. coli at 2.0 Å.
J Mol Biol 362 :933-942.
PubMed Id: 16949612.
OmpC Osmoporin clinical variant OmpC06: Escherichia coli  B Bacteria, 2.50 Å
Clinical variant OmpC20, 2.50 Å: 2XE2
Clinical variant OmpC26, 2.28 Å: 2XE5
Clinical variant OmpC28, 2.85 Å: 2XE3
Clinical variant OmpC33, 3.47 Å: 2XG6
Lou et al. (2011).
Lou H, Chen M, Black SS, Bushell SR, Ceccarelli M, Mach T, Beis K, Low AS, Bamford VA, Booth IR, Bayley H, & Naismith JH (2011). Altered antibiotic transport in OmpC mutants isolated from a series of clinical strains of multi-drug resistant E. coli.
PLoS One 6 :e25825.
PubMed Id: 22053181.
doi: 10.1371/journal.pone.0025825.
OmpC homolog (OmpE36) with bound lipopolysaccharide (LPS): Enterobacter cloacae  B Bacteria (expressed in E. coli), 1.45 Å
Arunmanee et al. (2016).
Arunmanee W, Pathania M, Solovyova AS, Le Brun AP, Ridley H, Baslé A, van den Berg B, & Lakey JH (2016). Gram-negative trimeric porins have specific LPS binding sites that are essential for porin biogenesis.
Proc Natl Acad Sci USA 113 34:E5034-E5043.
PubMed Id: 27493217.
doi: 10.1073/pnas.1602382113.
OmpG *monomeric* porin: Escherichia coli  B Bacteria, 2.3 Å
Subbarao and van den Berg (2006).
Subbarao GV & van den Berg B (2006). Crystal structure of the monomeric porin OmpG.
J Mol Biol 360 :750-759.
PubMed Id: 16797588.
OmpG *monomeric* porin in open state: Escherichia coli  B Bacteria, 2.3 Å
OmpG in closed state, 2.73 Å: 2IWW
Yildiz et al. (2006).
Yildiz O, Vinothkumar KR, Goswami P, & Kuhlbrandt W (2006). Structure of the monomeric outer-membrane porin OmpG in the open and closed conformation.
EMBO J. 25 :3702-3713.
PubMed Id: 16888630.
OmpG *monomeric* porin: Escherichia coli  B Bacteria, 2.18 Å
His231A/His261A mutant stable in open state
Korkmaz-Ozkan et al. (2010).
Korkmaz-Özkan F, Köster S, Kühlbrandt W, Mäntele W, & Yildiz O (2010). Correlation between the OmpG secondary structure and its pH-dependent alterations monitored by FTIR.
J Mol Biol 401 :56-67.
PubMed Id: 20561532.
doi: 10.1016/j.jmb.2010.06.015.
OmpG *monomeric* porin: Escherichia coli  B Bacteria, NMR Structure (DPC micelles)
Liang & Tamm (2007).
Liang B & Tamm LK (2007). Structure of outer membrane protein G by solution NMR Spectroscopy.
Proc Natl Acad Sci USA 104 :16140-16145.
PubMed Id: 17911261.
OmpG *monomeric* porin: Escherichia coli  B Bacteria, solid-state NMR structure
protein embedded in E. coli lipid extracts
Retel et al. (2017).
Retel JS, Nieuwkoop AJ, Hiller M, Higman VA, Barbet-Massin E, Stanek J, Andreas LB, Franks WT, van Rossum BJ, Vinothkumar KR, Handel L, de Palma GG, Bardiaux B, Pintacuda G, Emsley L, Kühlbrandt W, & Oschkinat H (2017). Structure of outer membrane protein G in lipid bilayers.
Nat Commun 8 1:2073.
PubMed Id: 29233991.
doi: 10.1038/s41467-017-02228-2.
OmpT porin (outer membrane expressed): Vibrio cholerae  B Bacteria, 3.2 Å
in vitro folded (monomeric), 1.66 Å: 6EHD
in vitro folded (trimeric), 2.72 Å: 6EHF
OmpTΔL8, 2.31 Å: 6EHE
Pathania et al. (2018).
Pathania M, Acosta-Gutierrez S, Bhamidimarri SP, Baslé A, Winterhalter M, Ceccarelli M, & van den Berg B (2018). Unusual Constriction Zones in the Major Porins OmpU and OmpT from Vibrio cholerae.
Structure 26 5:708-721.e4.
PubMed Id: 29657131.
doi: 10.1016/j.str.2018.03.010.
OmpU: Vibrio cholerae  B Bacteria (expressed in E. coli), 2.22 Å
Li et al. (2018).
Li H, Zhang W, & Dong C (2018). Crystal structure of the outer membrane protein OmpU from Vibrio cholerae at 2.2 Å resolution.
Acta Crystallogr D Struct Biol 74 :21-29.
PubMed Id: 29372896.
doi: 10.1107/S2059798317017697.
OmpU porin: Vibrio cholerae  B Bacteria (expressed in E. coli), 1.55 Å
OmpU ΔN, 2.02 Å: 6EHC
Pathania et al. (2018).
Pathania M, Acosta-Gutierrez S, Bhamidimarri SP, Baslé A, Winterhalter M, Ceccarelli M, & van den Berg B (2018). Unusual Constriction Zones in the Major Porins OmpU and OmpT from Vibrio cholerae.
Structure 26 5:708-721.e4.
PubMed Id: 29657131.
doi: 10.1016/j.str.2018.03.010.
PhoE: Escherichia coli  B Bacteria, 3.0 Å
Cowan et al. (1992).
Cowan SW, Schirmer T, Rummel G, Steiert M, Ghosh R, Pauptit RA, Jansonius JN, & Rosenbusch JP (1992). Crystal structures explain functional properties of two Escherichia coli porins.
Nature 358 :727-733.
PubMed Id: 1380671.
LamB Maltoporin: Salmonella typhimurium  B Bacteria, 2.4 Å
Meyer et al. (1997).
Meyer JEW, Hofnung M, & Schulz GE (1997). Structure of maltoporin from Salmonella typhimurium ligated with a nitrophenyl-maltotrioside.
J. Mol. Biol 266 :761-775.
PubMed Id: 9102468.
LamB Maltoporin: Escherichia coli  B Bacteria, 3.1 Å
Schirmer et al. (1995).
Schirmer T, Keller TA, Wang YF, & Rosenbusch JP (1995). Structural basis for sugar translocation through maltoporin channels at 3.1 Å resolution.
Science 267 :512-4.
PubMed Id: 7824948.
LamB Maltoporin in complex with maltose: Escherichia coli  B Bacteria, 2.6 Å
In complex with maltotriose, 3.20 Å: 1MPN
In complex with maltohexaose, 2.80 Å: 1MPO
Dutzler et al. (1996).
Dutzler R, Wang YF, Rizkallah P, Rosenbusch JP, Schirmer T (1996). Crystal structures of various maltooligosaccharides bound to maltoporin reveal a specific sugar translocation pathway.
Structure 4 :127-134.
PubMed Id: 8805519.
LamB Maltoporin in complex with sucrose: Escherichia coli  B Bacteria, 2.4 Å
In complex with trehalose, 3.0 Å: 1MPQ
Wang et al. (1997).
Wang YF, Dutzler R, Rizkallah PJ, Rosenbusch JP, & Schirmer T (1997). Channel specificity: structural basis for sugar discrimination and differential flux rates in maltoporin.
J Mol Biol 272 :56-63.
PubMed Id: 9299337.
ScrY sucrose-specific porin: Salmonella typhimurium  B Bacteria, 2.4 Å
Complexed Form, 1A0T.
Uncomplexed form, 1A0S.
Forst et al. (1998).
Forst D, Welte W, Wacker T, & Diederichs K (1998). Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose.
Nature Structural Biol 5 :37-46.
PubMed Id: 9437428.
MspA mycobacterial porin: Mycobacterium smegmatis  B Bacteria, 2.5 Å
Homooctamer
Faller et al. (2004).
Faller M, Niederweis M, & Schulz GE (2004). The structure of a mycobacterial outer-membrane channel.
Science 303 :1189-1192.
PubMed Id: 14976314.
OprB carbohydrate-specific transporter at high pH: Pseudomonas putida  B Bacteria (expressed in E. coli), 2.70 Å
low-pH structure, 3.10 Å: 4GF4
van den Berg (2012).
van den Berg B (2012). Structural basis for outer membrane sugar uptake in pseudomonads.
J Biol Chem 287 :41044-41052.
PubMed Id: 23066028.
doi: 10.1074/jbc.M112.408518.
OprO diphosphate-specific transporter: Pseudomonas aeruginosa  B Bacteria, 1.52 Å
F62Y/D114Y mutant, 1.54 Å: 4RJX
Modi et al. (2015).
Modi N, Ganguly S, Bárcena-Uribarri I, Benz R, van den Berg B, & Kleinekathöfer U (2015). Structure, Dynamics, and Substrate Specificity of the OprO Porin from Pseudomonas aeruginosa.
Biophys J 109 :1429-1438.
PubMed Id: 26445443.
doi: 10.1016/j.bpj.2015.07.035.
OprP phosphate-specific transporter: Pseudomonas aeruginosa  B Bacteria, 1.9 Å
Contains a novel nine-residue arginine ladder
Moraes et al. (2007).
Moraes TF, Bains M, Hancock REW & Strynadka NCJ (2007). An arginine ladder in OprP mediates phosphate-specific transfer across the outer membrane.
Nature Struc Mol Biol 14 :85-87.
PubMed Id: 17187075.
PorB outer membrane protein, native structure: Neisseria meningitidis  B Bacteria (expressed in E. coli), 2.30 Å
The second most common OMP of Neisseria, PorB is required for pathogenesis.
Former 3A2R, 3A2T, and 3A2U superseded by 3VZT, 3VZW, and 3VZU, respectively.
In complex with sucrose, 2.20 Å: 3A2S
In complex with galactose, 3.20 Å: 3VZW
In complex with AMP-PNP, 2.90 Å: 3ZVU
Tanabe et al. (2010).
Tanabe M, Nimigean CM, & Iverson TM (2010). Structural basis for solute transport, nucleotide regulation, and immunological recognition of Neisseria meningitidis PorB.
Proc Natl Acad Sci USA 107 :6811-6816.
PubMed Id: 20351243.
KdgM *monomeric* porin in complex with disordered oligogalacturonate: Dickeya dadantii  B Bacteria (expressed in E. coli), 2.10 Å
Hutter et al. (2014).
Hutter CA, Lehner R, Wirth Ch, Condemine G, Peneff C, & Schirmer T (2014). Structure of the oligogalacturonate-specific KdgM porin.
Acta Crystallogr. D Biol. Crystallogr. 70 :1770-1778.
PubMed Id: 24914987.
doi: 10.1107/S1399004714007147.
CymA monomeric outer membrane protein (NHis-SeMet): Klebsiella oxytoca  B Bacteria (expressed in E. coli), 2.51 Å
NHis-native, 1.83 Å: 4V3H
wild-type, 2.30 Å: 4D51
&alfa;-cyclodextrin soak, 1.70 Å: 4D5B
β-cyclodextrin soak, 1.90 Å: 4D5D
van den Berg et al. (2015).
van den Berg B, Prathyusha Bhamidimarri S, Dahyabhai Prajapati J, Kleinekathöfer U, & Winterhalter M (2015). Outer-membrane translocation of bulky small molecules by passive diffusion.
Proc Natl Acad Sci USA 112 :E2991-E2999.
PubMed Id: 26015567.
doi: 10.1073/pnas.1424835112.
COG4313 outer membrane channel: Pseudomonas putida  B Bacteria (expressed in E. coli), 2.30 Å
van den Berg et al. (2015).
van den Berg B, Bhamidimarri SP, & Winterhalter M (2015). Crystal structure of a COG4313 outer membrane channel.
Sci Rep 5 :11927.
PubMed Id: 26149193.
doi: 10.1038/srep11927.
OprG outer membrane amino acid transporter: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), NMR structure
P92A mutant, NMR structure: 2N6P
Kucharska et al. (2015).
Kucharska I, Seelheim P, Edrington T, Liang B, & Tamm LK (2015). OprG Harnesses the Dynamics of its Extracellular Loops to Transport Small Amino Acids across the Outer Membrane of Pseudomonas aeruginosa.
Structure 23 :2234-2245.
PubMed Id: 26655471.
doi: 10.1016/j.str.2015.10.009.
MOMP major outer membrane protein: Campylobacter jejuni (expressed in E. coli), 2.1 Å
expressed in C. jejuni, 2.88 Å: 5LDT
Ferrara et al. (2016).
Ferrara LG, Wallat GD, Moynié L, Dhanasekar NN, Aliouane S, Acosta-Gutiérrez S, Pagès JM, Bolla JM, Winterhalter M, Ceccarelli M, & Naismith JH (2016). MOMP from Campylobacter jejuni Is a Trimer of 18-Stranded β-Barrel Monomers with a Ca 2+ Ion Bound at the Constriction Zone.
J Mol Biol 428 :4528-4543.
PubMed Id: 27693650.
doi: 10.1016/j.jmb.2016.09.021.
Omp-Pst1 type-A porin: Providencia stuartii  B Bacteria (expressed in E. coli), 3.2 Å
Structures reveal that these porins can self-associate to form dimers of trimers
Omp-Pst1 type-B, 2.7 Å: 5NXR
Omp-Pst1 type-B in complex with maltose, 3 Å: 5NXU
Omp-Pst2 reveals dimer of trimers, 2.2 Å: 4D65
283-LGNY-286, steric zipper that supports dimerization of Pst2, 0.997 Å: 5N9H
206-GVVTSE-211 steric zipper that supports dimerization of Pst1, 1.91 Å: 5N9I
Pst1 L5 deletion, 3.12 Å: 5NXN
El-Khatib et al. (2018).
El-Khatib M, Nasrallah C, Lopes J, Tran QT, Tetreau G, Basbous H, Fenel D, Gallet B, Lethier M, Bolla JM, Pagès JM, Vivaudou M, Weik M, Winterhalter M, & Colletier JP (2018). Porin self-association enables cell-to-cell contact inProvidencia stuartiifloating communities.
Proc Natl Acad Sci USA 115 10:E2220-E2228.
PubMed Id: 29476011.
doi: 10.1073/pnas.1714582115.
Chitoporin (ChiP), in vitro-folded crystal form I: Vibrio harveyi  B Bacteria (expressed in E. coli), 1.95 Å
in vitro-folded crystal form II, 3.08 Å: 5MDP
outer membrane (OM) expressed ChiP, 2.5 Å: 5MDQ
with chito-hexose, in vitro-folded 1.9 Å: 5MDR
with chito-tetraose OM-expressed, 2.6 Å: 5MDS
Aunkham et al. (2018).
Aunkham A, Zahn M, Kesireddy A, Pothula KR, Schulte A, Baslá A, Kleinekathöfer U, Suginta W, & van den Berg B (2018). Structural basis for chitin acquisition by marine Vibrio species.
Nat Commun 9 1.
PubMed Id: 29335469.
doi: 10.1038/s41467-017-02523-y.
Outer Membrane Carboxylate Channels (Occ)
These outer membrane proteins require substrates to have a carboxyl group for efficient transport.
OccD channels are selective for basic amino acids. OccK channels prefer cyclic substrates. See Eren et al. (2012).
OccD1 (OprD) basic amino acid uptake channel: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), 2.9 Å
Biswas et al. (2007).
Biswas S, Mohammad MM, Patel DR, Movileanu L, & van den Berg B (2007). Structural insight into OprD substrate specificity.
Nature Struct Mol Biol 14 :1108-1109.
PubMed Id: 17952093.
OccD1 (OprD) basic amino acid uptake channel: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), 2.15 Å
Eren et al. (2012).
Eren E, Vijayaraghavan J, Liu J, Cheneke BR, Touw DS, Lepore BW, Indic M, Movileanu L, & van den Berg B (2012). Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
PLoS Biol 10 :e1001242.
PubMed Id: 22272184.
doi: 10.1371/journal.pbio.1001242.
OccD2 (OpdC) basic amino acid uptake channel: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), 2.80 Å
Eren et al. (2012).
Eren E, Vijayaraghavan J, Liu J, Cheneke BR, Touw DS, Lepore BW, Indic M, Movileanu L, & van den Berg B (2012). Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
PLoS Biol 10 :e1001242.
PubMed Id: 22272184.
doi: 10.1371/journal.pbio.1001242.
OccD3 (OpdP) basic amino acid uptake channel: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), 2.70 Å
Eren et al. (2012).
Eren E, Vijayaraghavan J, Liu J, Cheneke BR, Touw DS, Lepore BW, Indic M, Movileanu L, & van den Berg B (2012). Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
PLoS Biol 10 :e1001242.
PubMed Id: 22272184.
doi: 10.1371/journal.pbio.1001242.
OccK1 (OpdK) benzoate channel: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), 2.8 Å
Binds vanillate. Forms labile trimer.
Biswas et al. (2008).
Biswas S, Mohammad MM, Movileanu L, & van den Berg B (2008). Crystal structure of the outer membrane protein OpdK from Pseudomonas aeruginosa.
Structure 16 :1027-1035.
PubMed Id: 18611376.
OccK1 (OpdK) benzoate channel: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), 1.65 Å
Eren et al. (2012).
Eren E, Vijayaraghavan J, Liu J, Cheneke BR, Touw DS, Lepore BW, Indic M, Movileanu L, & van den Berg B (2012). Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
PLoS Biol 10 :e1001242.
PubMed Id: 22272184.
doi: 10.1371/journal.pbio.1001242.
OccK2 (OpdF) glucuronate channel: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), 2.30 Å
Eren et al. (2012).
Eren E, Vijayaraghavan J, Liu J, Cheneke BR, Touw DS, Lepore BW, Indic M, Movileanu L, & van den Berg B (2012). Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
PLoS Biol 10 :e1001242.
PubMed Id: 22272184.
doi: 10.1371/journal.pbio.1001242.
OccK3 (OpdO) aromatic hydrocarbon channel: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), 1.45 Å
Eren et al. (2012).
Eren E, Vijayaraghavan J, Liu J, Cheneke BR, Touw DS, Lepore BW, Indic M, Movileanu L, & van den Berg B (2012). Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
PLoS Biol 10 :e1001242.
PubMed Id: 22272184.
doi: 10.1371/journal.pbio.1001242.
OccK4 (OpdL) aromatic hydrocarbon channel: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), 2.10 Å
Eren et al. (2012).
Eren E, Vijayaraghavan J, Liu J, Cheneke BR, Touw DS, Lepore BW, Indic M, Movileanu L, & van den Berg B (2012). Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
PLoS Biol 10 :e1001242.
PubMed Id: 22272184.
doi: 10.1371/journal.pbio.1001242.
OccK5 (OpdH) aromatic hydrocarbon channel: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), 2.60 Å
Eren et al. (2012).
Eren E, Vijayaraghavan J, Liu J, Cheneke BR, Touw DS, Lepore BW, Indic M, Movileanu L, & van den Berg B (2012). Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
PLoS Biol 10 :e1001242.
PubMed Id: 22272184.
doi: 10.1371/journal.pbio.1001242.
OccK6 (OpdQ) aromatic hydrocarbon channel: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), 2.35 Å
Eren et al. (2012).
Eren E, Vijayaraghavan J, Liu J, Cheneke BR, Touw DS, Lepore BW, Indic M, Movileanu L, & van den Berg B (2012). Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
PLoS Biol 10 :e1001242.
PubMed Id: 22272184.
doi: 10.1371/journal.pbio.1001242.
BenF-like Porin (putative) benzoate channel: Pseudomonas fluorescens  B Bacteria, 2.60 Å
Probably belongs to OccK subfamily
Sampathkumar et al. (2010).
Sampathkumar P, Lu F, Zhao X, Li Z, Gilmore J, Bain K, Rutter ME, Gheyi T, Schwinn KD, Bonanno JB, Pieper U, Fajardo JE, Fiser A, Almo SC, Swaminathan S, Chance MR, Baker D, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Sali A, Sauder JM, &Burley SK (2010). Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 Å resolution.
Proteins 78 :3056-3062.
PubMed Id: 20737437.
OccAB1 outer membrane channel: Acinetobacter baumannii  B Bacteria (expressed in E. coli), 2.05 Å
Zahn et al. (2016).
Zahn M, Bhamidimarri SP, Baslé A, Winterhalter M, & van den Berg B (2016). Structural Insights into Outer Membrane Permeability of Acinetobacter baumannii.
Structure 24 :221-231.
PubMed Id: 26805524.
doi: 10.1016/j.str.2015.12.009.
OccAB2 outer membrane channel: Acinetobacter baumannii  B Bacteria (expressed in E. coli), 2.9 Å
Zahn et al. (2016).
Zahn M, Bhamidimarri SP, Baslé A, Winterhalter M, & van den Berg B (2016). Structural Insights into Outer Membrane Permeability of Acinetobacter baumannii.
Structure 24 :221-231.
PubMed Id: 26805524.
doi: 10.1016/j.str.2015.12.009.
OccAB3 outer membrane channel: Acinetobacter baumannii  B Bacteria (expressed in E. coli), 1.75 Å
Zahn et al. (2016).
Zahn M, Bhamidimarri SP, Baslé A, Winterhalter M, & van den Berg B (2016). Structural Insights into Outer Membrane Permeability of Acinetobacter baumannii.
Structure 24 :221-231.
PubMed Id: 26805524.
doi: 10.1016/j.str.2015.12.009.
OccAB4 outer membrane channel: Acinetobacter baumannii  B Bacteria (expressed in E. coli), 2.2 Å
Zahn et al. (2016).
Zahn M, Bhamidimarri SP, Baslé A, Winterhalter M, & van den Berg B (2016). Structural Insights into Outer Membrane Permeability of Acinetobacter baumannii.
Structure 24 :221-231.
PubMed Id: 26805524.
doi: 10.1016/j.str.2015.12.009.
Beta-Barrel Membrane Proteins: Monomeric/Dimeric
TolC outer membrane protein: Escherichia coli  B Bacteria, 2.1 Å
NOTE: Functional protein is a homotrimer. Each monomer contributes 4 strands to a single barrel.
Koronakis et al. (2000).
Koronakis V, Sharff A, Koronakis E, Luisi B, & Hughes C (2000). Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export.
Nature 405 :914-919.
PubMed Id: 10879525.
TolC outer membrane protein, ligand blocked: Escherichia coli  B Bacteria, 2.75 Å
Higgins et al. (2004).
Higgins MK, Eswaran J, Edwards P, Schertler GF, Hughes C, & Koronakis V (2004). Structure of the ligand-blocked periplasmic entrance of the bacterial multidrug efflux protein TolC.
J Mol Biol 342 :697-702.
PubMed Id: 15342230.
TolC outer membrane protein (Y362F, R367E), partially open state: Escherichia coli  B Bacteria, 3.2 Å
2VDE is P2 12 12 1 form. C2 form, 3.30 Å: 2VDD
Bavro et al. (2008).
Bavro VN, Pietras Z, Furnham N, Pérez-Cano L, Fernández-Recio J, Pei XY, Misra R, & Luisi B (2008). Assembly and channel opening in a bacterial drug efflux machine.
Mol Cell 30 :114-121.
PubMed Id: 18406332.
CmeC bacterial multi-drug efflux transporter outer membrane channel: Campylobacter jejuni  B Bacteria, 2.37 Å
Su et al. (2014).
Su CC, Radhakrishnan A, Kumar N, Long F, Bolla JR, Lei HT, Delmar JA, Do SV, Chou TH, Rajashankar KR, Zhang Q, & Yu EW (2014). Crystal structure of the Campylobacter jejuni CmeC outer membrane channel.
Protein Sci 23 7:954-961.
PubMed Id: 24753291.
doi: 10.1002/pro.2478.
VceC outer membrane protein: Vibrio cholerae  B Bacteria, 1.8 Å
NOTE: Functional protein is a homotrimer. Each monomer contributes 4 strands to a single barrel.
Federici et al. (2005).
Federici L, Du D, Walas F, Matsumura H, Fernandez-Recio J, McKeegan KS, Borges-Walmsley MI, Luisi BF, & Walmsley AR (2005). The Crystal Structure of the Outer Membrane Protein VceC from the Bacterial Pathogen Vibrio cholerae at 1.8 A Resolution.
J Biol Chem 280 :15307-15314.
PubMed Id: 15684414.
OprM drug discharge outer membrane protein: Pseudomonas aeruginosa  B Bacteria, 2.56 Å
Functional protein is a homotrimer. Each monomer contributes 4 strands to a single barrel. H32 space group.
OprM is the discharge channel for the tripartite efflux complex MexAB-OprM. The structures of MexB (the inner membrane efflux pump) and MexA (periplasmic fusion protein) are known. See 2V50 and 1T5E, respectively.
Akama et al. (2004).
Akama H, Kanemaki M, Yoshimura M, Tsukihara T, Kashiwagi T, Yoneyama H, Narita S, Nakagawa A, & Nakae T (2004). Crystal structure of the drug discharge outer membrane protein, OprM, of Pseudomonas aeruginosa: dual modes of membrane anchoring and occluded cavity end.
J Biol Chem 279 :52816-52819.
PubMed Id: 15507433.
OprM drug discharge outer membrane protein: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), 2.40 Å
Structure of OprM in a non-symmetrical space group, P2 12 12 1
Phan et al. (2010).
Phan G, Benabdelhak H, Lascombe MB, Benas P, Rety S, Picard M, Ducruix A, Etchebest C, & Broutin I (2010). Structural and dynamical insights into the opening mechanism of P. aeruginosa OprM channel.
Structure 18 :507-517.
PubMed Id: 20399187.
OprN drug discharge outer membrane protein, I4 space group: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), 1.69 Å
P321 space group, 2.70 Å: 5AZP
Yonehara et al. (2016).
Yonehara R, Yamashita E, & Nakagawa A (2016). Crystal structures of OprN and OprJ, outer membrane factors of multidrug tripartite efflux pumps of Pseudomonas aeruginosa.
Proteins 84 6:759-769.
PubMed Id: 26914226.
doi: 10.1002/prot.25022.
OprJ drug discharge outer membrane protein: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), 3.10 Å
Yonehara et al. (2016).
Yonehara R, Yamashita E, & Nakagawa A (2016). Crystal structures of OprN and OprJ, outer membrane factors of multidrug tripartite efflux pumps of Pseudomonas aeruginosa.
Proteins 84 6:759-769.
PubMed Id: 26914226.
doi: 10.1002/prot.25022.
ST50 discharge outer membrane protein: Salmonella enterica  B Bacteria (expressed in E. coli), 2.98 Å
Functional protein is a homotrimer. Each monomer contributes 4 strands to a single barrel.
Guan et al. (2015).
Guan HH, Yoshimura M, Chuankhayan P, Lin CC, Chen NC, Yang MC, Ismail A, Fun HK, & Chen CJ (2015). Crystal structure of an antigenic outer-membrane protein from Salmonella Typhi suggests a potential antigenic loop and an efflux mechanism.
Sci Rep 5 :16441.
PubMed Id: 26563565.
doi: 10.1038/srep16441.
CusC heavy metal discharge outer membrane protein: Escherichia coli  B Bacteria, 2.30 Å
NOTE: Functional protein is a homotrimer. Each monomer contributes 4 strands to a single barrel. H32 space group.
Kulathila et al. (2011).
Kulathila R, Kulathila R, Indic M, & van den Berg B (2011). Crystal structure of Escherichia coli CusC, the outer membrane component of a heavy metal efflux pump.
PLoS One 6 :e15610.
PubMed Id: 21249122.
doi: 10.1371/journal.pone.0015610.
CusC heavy metal discharge outer membrane protein: Escherichia coli  B Bacteria, 2.09 Å
ΔC1 mutant, 2.53 Å: 4K7K
C1S mutant, 2.69 Å: 4K34
Lei et al. (2014).
Lei HT, Bolla JR, Bishop NR, Su CC, & Yu EW (2014). Crystal Structures of CusC Review Conformational Changes Accompanying Folding and Transmembrane Channel Formation.
J Mol Biol 426 :403-411.
PubMed Id: 24099674.
doi: 10.1016/j.jmb.2013.09.042.
apo BtuB cobalamin transporter: Escherichia coli  B Bacteria, 2.0 Å
Related structures:
1NQF (SeMet-BtuB),
1NQG (Ca 2+-BtuB),
1NQH (Ca 2+-B 12-BtuB).
Chimento et al. (2003).
Chimento DP, Mohanty AK, Kadner RJ, & Wiener MC (2003). Substrate-induced transmembrane signaling in the cobalamin transporter BtuB.
Nat Struct Biol. 10 :394-401.
PubMed Id: 12652322.
BtuB with bound colicin E3 R-domain: Escherichia coli  B Bacteria, 2.75 Å
NOTE: The 135-residue coiled-coil R-domain is believed to deliver the colicin to OmpF (above).
Kurisu et al. (2003).
Kurisu G, Zakharov SD, Zhalnina MV, Bano S, Eroukova VY, Rokitskaya TI, Antonenko YN, Wiener MC, & Cramer WA (2003). The structure of BtuB with bound colicin E3 R-domain implies a translocon.
Nat. Struct. Biol. 10 :948-954.
PubMed Id: 14528295.
apo BtuB by in meso crystallization: Escherichia coli  B Bacteria, 1.95 Å
NOTE: Crystals were prepared from cubic phase lipids. This is the first β-barrel protein prepared by this method.
Cherezov et al. (2006).
Cherezov V, Yamashita E, Liu W, Zhalnina M, Cramer WA & Caffrey M (2006). In meso structure of the cobalamin transporter, BtuB, at 1.95 Å resolution.
J Mol Biol 364 :716-734.
PubMed Id: 17028020.
BtuB in complex with TonB: Escherichia coli  B Bacteria, 2.1 Å
Shultis et al. (2006).
Shultis DD, Purdy MD, Banchs CN, & Wiener MC (2006). Outer membrane active transport: structure of the BtuB:TonB complex.
Science 312 :1396-1399.
PubMed Id: 16741124.
BtuB with bound colicin E2 R-domain: Escherichia coli  B Bacteria, 3.50 Å
Sharma et al. (2007).
Sharma O, Yamashita E, Zhalnina MV, Zakharov SD, Datsenko KA, Wanner BL, & Cramer WA (2007). Structure of the complex of the colicin E2 R-domain and its BtuB receptor. The outer membrane colicin translocon.
J Biol Chem 282 :23163-23170.
PubMed Id: 17548346.
apo BtuB V10R1 spin-labeled: Escherichia coli  B Bacteria, 2.44 Å
Spin-labeled BtuB V10R1 with bound calcium and cyanocobalamin, 2.44 Å: 3M8D
Freed et al. (2010).
Freed DM, Horanyi PS, Wiener MC, & Cafiso DS (2010). Conformational exchange in a membrane transport protein is altered in protein crystals.
Biophys J 99 :1604-1610.
PubMed Id: 20816073.
doi: 10.1016/j.bpj.2010.06.026.
Colicin I receptor Cir in complex with Colicin Ia binding domain: Escherichia coli  B Bacteria, 2.5 Å
Cir Colicin I receptor alone, 2.65 Å: 2HDF
Buchanan et al. (2007).
Buchanan S, Lukacik P, Grizot S, Ghirlando R, Ali MMU, Barnard TJ, Jakes S, Kienker PK, & Esser L. (2007). Structure of colicin I receptor bound to the R-domain of colicin Ia: Implications for protein import.
EMBO J 26 :2594-2604.
PubMed Id: 17464289.
OmpA: Escherichia coli  B Bacteria, 2.50 Å
Pautsch & Schulz (1998).
Pautsch A & Schulz GE (1998). Structure of the outer membrane protein A transmembrane domain.
Nature Struct Biol 5 :1013-1017.
PubMed Id: 9808047.
OmpA: Escherichia coli  B Bacteria, 1.60 Å
Pautsch & Schulz (2000).
Pautsch A & Schulz GE (2000). High-resolution structure of the OmpA membrane domain.
J Mol Biol 298 :273-282.
PubMed Id: 10764596.
OmpA: Escherichia coli  B Bacteria, NMR Structure
in DPC micelles
Arora et al. (2001).
Arora A, Abildgaard F, Bushweller JH, & Tamm LK (2001). Structure of outer membrane protein A transmembrane domain by NMR spectroscopy.
Nature Structural Biol. 8 :334-338.
PubMed Id: 11276254.
OmpA: Escherichia coli  B Bacteria, NMR structure
DPC micelles. High-resolution structure determined using residual dipolar couplings.
Cierpicki et al. (2006).
Cierpicki T, Liang B, Tamm LK, & Bushweller JH (2006). Increasing the accuracy of solution NMR structures of membrane proteins by application of residual dipolar couplings. High-resolution structure of outer membrane protein A.
J Am Chem Soc 128 :6947-6951.
PubMed Id: 16719475.
OmpA with four shortened loops: Escherichia coli  B Bacteria, NMR Structure
DHPC micelles. Called β-barrel platform (BBP).
Johansson et al. (2007).
Johansson MU, Alioth S, Hu K, Walser R, Koebnik R, & Pervushin K (2007). A minimal transmembrane β-barrel platform protein studied by nuclear magnetic resonance.
Biochemistry 46 :1128-1140.
PubMed Id: 17260943.
OmpA: Klebsiella pneumoniae  B Bacteria (expressed in E. coli), NMR Structure
DHPC micelles
Renault et al. (2009).
Renault M, Saurel O, Czaplicki J, Demange P, Gervais V, Löhr F, Réat V, Piotto M, & Milon A (2009). Solution state NMR structure and dynamics of KpOmpA, a 210 residue transmembrane domain possessing a high potential for immunological applications
J Mol Biol 385 :117-130.
PubMed Id: 18952100.
doi: 10.1016/j.jmb.2008.10.021.
OmpT outer membrane protease: Escherichia coli  B Bacteria, 2.6 Å
Vandeputte-Rutten et al. (2001).
Vandeputte-Rutten L, Kramer RA, Kroon J, Dekker N, Egmond, MR, & Gros P (2001). Crystal structure of the outer membrane protease OmpT from Eschericia coli suggests a novel catalytic site.
EMBO J 20 :5033-5039.
PubMed Id: 11566868.
Pla Plasminogen activator (native 1): Yersinia pestis  B Bacteria (expressed in E. coli), 1.90 Å
Wild-type (Native 2), 2.30 Å: 2X56
D86A mutant, 2.55 Å: 2X4M
Eren et al. (2010).
Eren E, Murphy M, Goguen J, & van den Berg B. (2010). An active site water network in the plasminogen activator Pla from Yersinia pestis.
Structure 18 :809-818.
PubMed Id: 20637417.
OmpW outer membrane protein: Escherichia coli  B Bacteria, 2.7 Å
2F1V is orthorhomibic form. Trigonal form, 3.0 Å: 2F1T
Hong et al. (2006).
Hong H, Patel DR, Tamm LK, & van den Berg B (2006). The Outer Membrane Protein OmpW Forms an Eight-stranded beta-Barrel with a Hydrophobic Channel.
J Biol Chem 281 :7568-7577.
PubMed Id: 16414958.
OmpW outer membrane protein: Escherichia coli  B Bacteria, NMR structure
30-Fos detergent
Horst et al. (2014).
Horst R, Stanczak P, & Wüthrich K (2014). NMR polypeptide backbone conformation of the E. coli outer membrane protein W.
Structure 22 :1204-1209.
PubMed Id: 25017731.
doi: 10.1016/j.str.2014.05.016.
CarO outer membrane protein, isoform 1: Acinetobacter baumannii  B Bacteria (expressed in E. coli), 2.70 Å
isoform 2, 2.70 Å: 4RLB
isoform 3, 2.15 Å: 4FUV
Zahn et al. (2015).
Zahn M, D'Agostino T, Eren E, Baslé A, Ceccarelli M, & van den Berg B (2015). Small-Molecule Transport by CarO, an Abundant Eight-Stranded β-Barrel Outer Membrane Protein from Acinetobacter baumannii.
J Mol Biol 427 :2329-2339.
PubMed Id: 25846137.
doi: 10.1016/j.jmb.2015.03.016.
OprG outer membrane protein: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), 2.4 Å
Potential channel for hydrophobic molecule transport
Touw et al. (2010).
Touw DS, Patel DR, & van den Berg B (2010). The crystal structure of OprG from Pseudomonas aeruginosa, a potential channel for transport of hydrophobic molecules across the outer membrane.
PLoS One 5 :e15016.
PubMed Id: 21124774.
doi: 10.1371/journal.pone.0015016.
OprH, outer membrane protein H: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), NMR Structure
Structure determined in DHPC micelles. Eight strands. Chemical-shift measurements identify likely lipopolysaccharide interaction sites.
Edrington et al. (2011).
Edrington TC, Kintz E, Goldberg JB, & Tamm LK (2011). Structural Basis for the Interaction of Lipopolysaccharide with Outer Membrane Protein H (OprH) from Pseudomonas aeruginosa
J Biol Chem 286 :39211-39223.
PubMed Id: 21865172.
doi: 10.1074/jbc.M111.280933.
OmpX: Escherichia coli  B Bacteria, 1.9 Å
Structure at 2.1 Å, 1QJ9
Vogt & Schulz (1999).
Vogt J & Schulz GE (1999). The structure of the outer membrane protein OmpX from Escherichia coli reveals possible mechanisms of virulence.
Structure Fold.Des. 7 :1301-1309.
PubMed Id: 10545325.
OmpX: Escherichia coli  B Bacteria, NMR (DHPC micelles)
Fernández et al. (2001).
Fernández C, Adeishvili K, & Wüthrich K (2001). Transverse relaxation-optimized NMR spectroscopy with the outer membrane protein OmpX in dihexanoyl phosphatidylcholine micelles.
Proc Natl Acad Sci USA 98 :2358-2363.
PubMed Id: 11226244.
OmpX: Escherichia coli  B Bacteria, NMR (DPC micelles, with H-bond constraints)
For structure without H-bond constraints, see 1Q9G
Fernández et al. (2004).
Fernández C, Hilty C, Wider G, Guntert P, & Wüthrich K (2004). NMR structure of the integral membrane protein OmpX.
J Mol Biol. 336 :1211-1221.
PubMed Id: 15037080.
OmpX in optimized nanodiscs: Escherichia coli  B Bacteria, NMR Structure
In DPC micelles, NMR Structure: 2M07
Hagn et al. (2013).
Hagn F, Etzkorn M, Raschle T, & Wagner G (2013). Optimized phospholipid bilayer nanodiscs facilitate high-resolution structure determination of membrane proteins.
J Am Chem Soc 135 :1919-1925.
PubMed Id: 23294159.
doi: 10.1021/ja310901f.
Ail adhesion protein: Yersinia pestis  B Bacteria (expressed in E. coli), 1.80 Å
In complex with sucrose octasulfate (SOS), 1.85 Å: 3QRC
Yamashita et al. (2011).
Yamashita S, Lukacik P, Barnard TJ, Noinaj N, Felek S, Tsang TM, Krukonis ES, Hinnebusch BJ, & Buchanan SK (2011). Structural Insights into Ail-Mediated Adhesion in Yersinia pestis.
Structure 19 :1672-1682.
PubMed Id: 22078566.
doi: 10.1016/j.str.2011.08.010.
Ail adhesion protein, decylphosphocholine micelles: Yersinia pestis  B Bacteria (expressed in E. coli), NMR structure
in decylphosphocholine micelles calculated with implicit membrane solvation, NMR structure: 2N2L
Marassi et al. (2015).
Marassi FM, Ding Y, Schwieters CD, Tian Y, & Yao Y (2015). Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation.
J Biomol NMR 63 :59-65.
PubMed Id: 26143069.
doi: 10.1007/s10858-015-9963-2.
Ail adhesion protein: Yersinia pestis  B Bacteria (expressed in E. coli), NMR structure
Structure of protein in phospholipid nano-disc. Examines the effect of KDO2-lipid A.
Dutta et al. (2017).
Dutta SK, Yao Y, & Marassi FM (2017). Structural Insights into the Yersinia pestis Outer Membrane Protein Ail in Lipid Bilayers.
J Phys Chem B 121 :7561-7570.
PubMed Id: 28726410.
doi: 10.1021/acs.jpcb.7b03941.
TtoA Outer Membrane Protein (OMP): Thermus thermophilus HB27  B Bacteria, 2.8 Å
First structure of an OMP from a thermophile
Brosig et al. (2009).
Brosig A, Nesper J, Boos W, Welte W, & Diederichs K (2009). Crystal structure of a major outer membrane protein from Thermus thermophilus HB27.
J Mol Biol 385 :1445-1455.
PubMed Id: 19101566.
OmpLA (PldA) outer membrane phospholipase A monomer: Escherichia coli  B Bacteria, 2.17 Å
Dimer, 2.10 Å: 1QD6
Snijder et al. (1999).
Snijder HJ, Ubarretxena-Belandia I, Blaauw M, Kalk KH, Verheij HM, Egmond MR, Dekker N, & Dijkstra BW (1999). Structural evidence for dimerization-regulated activation of an integral membrane phospholipase.
Nature 401 :717-721.
PubMed Id: 10537112.
OmpLA (PldA) outer membrane phospholipase A monomer with Ca++: Escherichia coli  B Bacteria, 2.60 Å
Dimer, 2.80 Å: 1FW3
Snijder et al. (2001).
Snijder HJ, Kingma RL, Kalk KH, Dekker N, Egmond MR, & Dijkstra BW (2001). Structural investigations of calcium binding and its role in activity and activation of outer membrane phospholipase A from Escherichia coli.
J Mol Biol 309 :477-489.
PubMed Id: 11371166.
OmpLA (PldA) active-site mutant (N156A), pH 6.1: Escherichia coli  B Bacteria, 2.50 Å
pH 4.6, 2.80 Å: 1ILD
pH 8.3, 2.98 Å: 1IM0
Snijder et al. (2001).
Snijder HJ, Van Eerde JH, Kingma RL, Kalk KH, Dekker N, Egmond MR, & Dijkstra BW (2001). Structural investigations of the active-site mutant Asn156Ala of outer membrane phospholipase A: function of the Asn-His interaction in the catalytic triad.
Protein Sci 10 :1962-1969.
PubMed Id: 11567087.
OpcA adhesin protein: Neisseria meningitidis  B Bacteria, 2.0 Å
Prince et al. (2002).
Prince SM, Achtman M, & Derrick JP (2002). Crystal structure of the OpcA integral membrane adhesin from Neisseria meningitidis.
Proc. Natl. Acad. Sci. USA 99 :3417-3421.
PubMed Id: 11891340.
OpcA adhesin protein: Neisseria meningitidis  B Bacteria (expressed in E. coli), 1.95 Å
In meso crystallization
Cherezov et al. (2008).
Cherezov V, Liu W, Derrick JP, Luan B, Aksimentiev A, Katritch V, & Caffrey M (2008). In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin.
Proteins 71 :24-34.
PubMed Id: 18076035.
doi: 10.1002/prot.21841.
NspA surface protein: Neisseria meningitidis  B Bacteria, 2.55 Å
Vandeputte-Rutten et al. (2003).
Vandeputte-Rutten L, Bos MP, Tommassen J, & Gros P (2003). Crystal structure of Neisserial surface protein A (NspA), a conserved outer membrane protein with vaccine potential.
J. Biol. Chem. 278 :24825-24830.
PubMed Id: 12716881.
NanC Porin, model for KdgM porin family: Escherichia coli  B Bacteria, 1.80 Å
H3 space group. See also 2WJQ, p6 322 space group, 2.0 Å resolution.
Wirth et al. (2009).
Wirth C, Condemine G, Boiteux C, Bernèche S, Schirmer T, & Peneff CM (2009). NanC Crystal Structure, a Model for Outer-Membrane Channels of the Acidic Sugar-Specific KdgM Porin Family.
J Mol Biol 394 :718-731.
PubMed Id: 19796645.
PagL LPS 3-O-deacylase: Pseudomonas aeruginosa  B Bacteria, 2.00 Å
Rutten et al. (2006).
Rutten L, Geurtsen J, Lambert W, Smolenaers JJ, Bonvin AM, de Haan A, van der Ley P, Egmond MR, Gros P, & Tommassen J (2006). Crystal structure and catalytic mechanism of the LPS 3-O-deacylase PagL from Pseudomonas aeruginosa.
Proc Natl Acad Sci USA 103 :7071-7076.
PubMed Id: 16632613.
doi: 10.1073/pnas.0509392103.
LpxR lipid A deacylase: Salmonella typhimurium  B Bacteria (expressed in E. coli), 1.90 Å
Rutten et al. (2009).
Rutten L, Mannie JP, Stead CM, Raetz CR, Reynolds CM, Bonvin AM, Tommassen JP, Egmond MR, Trent MS, & Gros P (2009). Active-site architecture and catalytic mechanism of the lipid A deacylase LpxR of Salmonella typhimurium.
Proc Natl Acad Sci USA 106 :1960-1964.
PubMed Id: 19174515.
doi: 10.1073/pnas.0813064106 .
PagP outer membrane palimitoyl transferease: Escherichia coli  B Bacteria, NMR
1MM4 is Structure in DPC micelles. Structure in OG micelles: 1MM5
Hwang et al. (2002).
Hwang PM, Choy WY, Lo EI, Chen L, Forman-Kay JD, Raetz CR, Privé GG, Bishop RE, Kay LE (2002). Solution structure and dynamics of the outer membrane enzyme PagP by NMR.
Proc Natl Acad Sci USA 99 :13560-13565.
PubMed Id: 12357033.
PagP outer membrane palimitoyl transferease: Escherichia coli  B Bacteria, 1.90 Å
Ahn et al. (2004).
Ahn VE, Lo EI, Engel CK, Chen L, Hwang PM, Kay LE, Bishop RE, & Prive GG (2004). A hydrocarbon ruler measures palmitate in the enzymatic acylation of endotoxin.
EMBO J. 23 :2931-2941.
PubMed Id: 15272304.
PagP outer membrane palimitoyl transferease crystallized from SDS/Co-solvent: Escherichia coli  B Bacteria, 1.40 Å
Reveals phospholipid access route (crenel between strands F and G)
Cuesta-Seijo et al. (2010).
Cuesta-Seijo JA, Neale C, Khan MA, Moktar J, Tran CD, Bishop RE, Pomès R, & Privé GG (2010). PagP crystallized from SDS/cosolvent reveals the route for phospholipid access to the hydrocarbon ruler.
Structure 18 :1210-1219.
PubMed Id: 20826347.
FadL long-chain fatty acid transporter: Escherichia coli  B Bacteria, 2.6 Å
1T16 is from Monoclinic crystals. From hexagonal crystals, 2.8 Å: 1T1L
van den Berg et al. (2004).
van den Berg B, Black PN, Clemons WM Jr, & Rapoport TA (2004). Crystal structure of the long-chain fatty acid transporter FadL.
Science 304 :1506-1509.
PubMed Id: 15178802.
FadL long-chain fatty acid transporter A77E/S100R mutant: Escherichia coli  B Bacteria, 2.5 Å
Mutants show that channel wall opening for passage of fatty acids into inner layer of outer membrane is likely.
ΔS3 kink, 2.60 Å: 2R88
P34A mutant, 3.3 Å: 2R4L
N33A mutant, 3.2 Å: 2R4N
ΔNPA mutant, 3.6 Å: 2R4O
G212E mutant, 2.9 Å: 2R4P
Hearn et al. (2009).
Hearn EM, Patel DR, Lepore BW, Indic M, van den Berg B (2009). Transmembrane passage of hydrophobic compounds through a protein channel wall.
Nature 458 :367-370.
PubMed Id: 19182779.
FadL long-chain fatty acid transporter D348R mutant: Escherichia coli  B Bacteria, 2.60 Å
This and associated structures in conjunction with in vivo transport assays and Trp fluorescence demonstrate ligand gating of the β-barrel protein.
delta N3 mutant, 3.40 Å: 2R89
D348A mutant, 2.70 Å: 3PF1
F3E mutant, 1.70 Å: 3PGU
F3G mutant, 1.90 Å: 3PGS
Lepore et al. (2011).
Lepore BW, Indic M, Pham H, Hearn EM, Patel DR, & van den Berg B (2011). Ligand-gated diffusion across the bacterial outer membrane
Proc Natl Acad Sci USA 108 :10121-10126.
PubMed Id: 21593406.
doi: 10.1073/pnas.1018532108.
FadL homologue long-chain fatty acid transporter: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), 2.2 Å
Shows break in channel wall for passage of fatty acids into inner layer of outer membrane in a species other than E. coli. Residues 22-463.
Hearn et al. (2009).
Hearn EM, Patel DR, Lepore BW, Indic M, van den Berg B (2009). Transmembrane passage of hydrophobic compounds through a protein channel wall.
Nature 458 :367-370.
PubMed Id: 19182779.
FauA alcaligin outer membrane transporter: Bordetella pertussis  B Bacteria (expressed in E. coli), 2.3 Å
Brillet et al. (2009).
Brillet K, Meksem A, Lauber E, Reimmann & C, Cobessi D (2009). Use of an in-house approach to study the three-dimensional structures of various outer membrane proteins: structure of the alcaligin outer membrane transporter FauA from Bordetella pertussis.
Acta Crystallogr D Biol Crystallogr 65 :326-331.
PubMed Id: 19307713.
TodX hydrocarbon transporter: Pseudomonas putida  B Bacteria, 2.6 Å
3BS0 is P1 space group, 2 molecules in asymmetric unit. I222 space group, 3.2 Å: 3BRZ
Hearn et al. (2008).
Hearn EM, Patel DR, & van den Berg BO (2008). Outer-membrane transport of aromatic hydrocarbons as a first step in biodegradation.
Proc Natl Acad Sci USA 105 :8601-8606.
PubMed Id: 18559855.
TbuX hydrocarbon transporter: Ralstonia pickettii  B Bacteria, 3.2 Å
Hearn et al. (2008).
Hearn EM, Patel DR, & van den Berg BO (2008). Outer-membrane transport of aromatic hydrocarbons as a first step in biodegradation.
Proc Natl Acad Sci USA 105 :8601-8606.
PubMed Id: 18559855.
Tsx nucleoside transporter (apoprotein): Escherichia coli  B Bacteria, 3.0 Å
Protein + thymidine, 3.10 Å: 1TLW
Protein + uridine, 3.10 Å: 1TLZ
Ye and van den Berg (2004).
Ye J & van den Berg B (2004). Crystal structure of the bacterial nucleoside transporter Tsx.
EMBO J. 23 :3187-3195.
PubMed Id: 15272310.
FhuA, Ferrichrome-iron receptor without ligand: Escherichia coli  B Bacteria, 2.7 Å
With ligand: 1BY5
Locher et al. (1998).
Locher KP, Rees B, Koebnik R, Mitschler A, Moulinier L, Rosenbusch JP, & Moras D (1998). Transmembrane signaling across the ligand-gated FhuA receptor: crystal structures of free and ferrichrome-bound states reveal allosteric changes.
Cell 11 :771-8.
PubMed Id: 9865695.
FhuA: Escherichia coli  B Bacteria, 2.50 Å
Includes the structure of a bound lipopolysaccharide (LPS) molecule
In complex with ferrichrome-iron, 2.70 Å: 1FCP
Ferguson et al. (1998).
Ferguson AD, Hofmann E, Coulton JW, Diederichs K, & Welte W (1998). Siderophore-mediated iron transport: crystal structure of FhuA with bound lipopolysaccharide.
Protein Sci 9 :956-963.
PubMed Id: 9856937.
FhuA-AW140-LPS: Escherichia coli  B Bacteria, 2.5 Å
Structure of lipopolysaccharide (LPS) in complex with FhuA.
FhuA-DL41-LPS-ferricrocin, 2.7 Å: 1QFF
Ferguson et al. (2000).
Ferguson AD, Welte W, Hofmann E, Lindner B, Holst O, Coulton JW, & Diederichs K (2000). A conserved structural motif for lipopolysaccharide recognition by procaryotic and eucaryotic proteins.
Structure 8 :585-592.
PubMed Id: 10873859.
FhuA in complex with albomycin: Escherichia coli  B Bacteria, 3.10 Å
In complex with phenylferricrocin, 2.95 Å: 1QJQ
Ferguson et al. (2000).
Ferguson AD, Braun V, Fiedler HP, Coulton JW, Diederichs K, & Welte W (2000). Crystal structure of the antibiotic albomycin in complex with the outer membrane transporter FhuA.
Science 282 :2215-2220.
PubMed Id: 10850805.
FhuA in complex with lipopolysaccharide and rifamycin CGP4832: Escherichia coli  B Bacteria, 2.90 Å
Ferguson et al. (2001).
Ferguson AD, Ködding J, Walker G, Bös C, Coulton JW, Diederichs K, Braun V, & Welte W (2001). Active transport of an antibiotic rifamycin derivative by the outer-membrane protein FhuA.
Structure 9 :707-716.
PubMed Id: 11587645.
FhuA in complex withTonB: Escherichia coli  B Bacteria, 3.3 Å
Pawelek et al. (2006).
Pawelek PD, Croteau N, Ng-Thow-Hing C, Khursigara CM, Moiseeva N, Allaire M, & Coulton JW (2006). Structure of TonB in complex with FhuA, E. coli outer membrane receptor.
Science 312 :1399-1402.
PubMed Id: 16741125.
FepA, Ferric enterobactin receptor: Escherichia coli  B Bacteria, 2.4 Å
Buchanan et al. (1999).
Buchanan S, Smith BS, Venkatramani L, Xia D, Esser L, Palnitkar M, Chakraborty R, van der Helm D, & Deisenhofer J. (1999). Crystal Structure of the outer membrane active transporter FepA from Escherichia coli.
Nature Structural Biol 6 :56-63.
PubMed Id: 9886293.
FecA, siderophore transporter: Escherichia coli  B Bacteria, 2.0 Å
Structure at 2.5 Å: 1KMP
Ferguson et al. (2002).
Ferguson AD, Chakraborty R, Smith BS, Esser L, van der Helm D, & Deisenhofer, J (2002). Structural basis of gating by the outer Membrane transporter FecA.
Science 295 :1715-1719.
PubMed Id: 11872840.
FecA, siderophore transporter (no ligand): Escherichia coli  B Bacteria, 2.5 Å
FecA with iron-free dicitrate, 2.15 Å: : 1PO0
FecA with diferric dicitrate, 3.4 Å: : 1PO3
Yue et al. (2003).
Yue WW, Grizot S, & Buchanan SK (2003). Structural evidence for iron-free citrate and ferric citrate binding to the TonB-dependent outer membrane transporter FecA.
J Mol Biol 332 :353-368.
PubMed Id: 12948487.
FecA, siderophore transporter periplasmic signalling domain: Escherichia coli  B Bacteria, NMR Structure
Shows the signalling domain not seen x-ray structures
Garcia-Herrero & Vogel (2005).
Garcia-Herrero A & Vogel HJ (2005). Nuclear magnetic resonance solution structure of the periplasmic signalling domain of the TonB-dependent outer membrane transporter FecA from Escherichia coli.
Mol Microbiol 58 :1226-1237.
PubMed Id: 16313612.
HasR heme-uptake receptor in complex with HasA hemophore and heme: Serratia marcescens  B Bacteria (expressed in E. coli), 2.7 Å
HasA~HasR, 3.0 Å: 3CSN
HasA~HasR[I671G]~heme, 2.8 Å: 3DDR
Krieg et al. (2009).
Krieg S, Huché F, Diederichs K, Izadi-Pruneyre N, Lecroisey A, Wandersman C, Delepelaire P, & Welte W. (2009). Heme uptake across the outer membrane as revealed by crystal structures of the receptor-hemophore complex.
Proc Natl Acad Sci USA 106 :1045-1050.
PubMed Id: 19144921.
ShuA heme-uptake receptor in complex with HasA hemophore and heme: Shigella dysenteriae  B Bacteria (expressed in E. coli), 2.6 Å
Cobessi et al. (2010).
Cobessi D, Meksem A, & Brillet K (2010). Structure of the heme/hemoglobin outer membrane receptor ShuA from Shigella dysenteriae: heme binding by an induced fit mechanism.
Proteins 78 :286-294.
PubMed Id: 19731368.
doi: 10.1002/prot.22539.
FptA, pyochelin outer membrane receptor: Pseudomonas aeruginosa  B Bacteria, 2.0 Å
Cobessi et al. (2005).
Cobessi D, Celia H, Pattus F (2005). Crystal structure at high resolution of ferric-pyochelin and its membrane receptor FptA from Pseudomonas aeruginosa.
J Mol Biol 352 :893-904.
PubMed Id: 16139844.
FpvA, Pyoverdine receptor: Pseudomonas aeruginosa  B Bacteria, 3.6 Å
Cobessi et al. (2005).
Cobessi D, Celia H, Folschweiller N, Schaik IJ, Abdallah MA, & Pattus F (2005). The crystal structure of the pyoverdine outer membrane receptor FpvA from Pseudomonas aeruginosa at 3.6 Å resolution.
J Mol Biol 347 :121-134.
PubMed Id: 15733922.
FpvA, Pyoverdine receptor (apo form): Pseudomonas aeruginosa  B Bacteria, 2.77 Å
Brillet et al. (2007).
Brillet K, Journet L, Célia H, Paulus L, Stahl A, Pattus F, & Cobessi D (2007). A β strand lock exchange for signal transduction in TonB-dependent transducers on the basis of a common structural motif.
Structure 15 :1383-1391.
PubMed Id: 17997964.
FpvA, Full-length structure bound to iron-pyoverdine: Pseudomonas aeruginosa  B Bacteria, 2.73 Å
Wirth et al. (2007).
Wirth C, Meyer-Klaucke W, Pattus F, & Cobessi D (2007). From the periplasmic signaling domain to the extracellular face of an outer membrane signal transducer of Pseudomonas aeruginosa: crystal structure of the ferric pyoverdine outer membrane receptor.
J Mol Biol 368 :398-406.
PubMed Id: 17349657.
AlgE alginate export protein: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), 2.30 Å
18-stranded β-barrel with a highly electropositive pore constriction that acts as a selectivity filter for negatively charged alginate.
Whitney et al. (2011).
Whitney JC, Hay ID, Li C, Eckford PD, Robinson H, Amaya MF, Wood LF, Ohman DE, Bear CE, Rehm BH, & Lynne Howell P (2011). Structural basis for alginate secretion across the bacterial outer membrane.
Proc Natl Acad Sci USA 108 :13083-13088.
PubMed Id: 21778407.
doi: 10.1073/pnas.1104984108.
AlgE alginate export protein: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), 1.90 Å
In meso crystallization.
Crystal form 2, 2.80 Å: 4AZL
Crystal form 3, 2.40 Å: 4B61
Tan et al. (2014).
Tan J, Rouse SL, Li D, Pye VE, Vogeley L, Brinth AR, El Arnaout T, Whitney JC, Howell PL, Sansom MS, & Caffrey M (2014). A conformational landscape for alginate secretion across the outer membrane of Pseudomonas aeruginosa.
Acta Crystallogr D Biol Crystallogr 70 :2054-2068.
PubMed Id: 25084326.
doi: 10.1107/S1399004714001850.
AlgE alginate export protein at 100 K: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), 2.90 Å
data collected at 293 K, 2.80 Å: 4XNK
Structures determined by serial x-ray crystallography
Huang et al. (2015).
Huang CY, Olieric V, Ma P, Panepucci E, Diederichs K, Wang M, & Caffrey M (2015). In meso in situ serial X-ray crystallography of soluble and membrane proteins.
Acta Crystallogr D Biol Crystallogr 71 :1238-1256.
PubMed Id: 26057665.
doi: 10.1107/S1399004715005210.
P pilus usher translocation domain, PapC130-640: Escherichia coli  B Bacteria, 3.2 Å
Remaut et al. (2008).
Remaut H, Tang C, Henderson NS, Pinkner JS, Wang T, Hultgren SJ, Thanassi DG, Waksman G, & Li H (2008). Fiber formation across the bacterial outer membrane by the chaperone/usher pathway.
Cell 133 :640-652.
PubMed Id: 18485872.
P pilus FimD usher bound to FimC:FimH substrate: Escherichia coli  B Bacteria, 2.80 Å
FimD translocation domain, 3.01 Å: 3OHN
Phan et al. (2011).
Phan G, Remaut H, Wang T, Allen WJ, Pirker KF, Lebedev A, Henderson NS, Geibel S, Volkan E, Yan J, Kunze MB, Pinkner JS, Ford B, Kay CW, Li H, Hultgren SJ, Thanassi DG, & Waksman G (2011). Crystal structure of the FimD usher bound to its cognate FimC-FimH substrate.
Nature 474 :49-53.
PubMed Id: 21637253.
doi: 10.1038/nature10109.
P pilus FimD usher in complex with FimC:FimF:FimG:FimH: Escherichia coli  B Bacteria, 3.80 Å
This is the complete structure of the tip complex assembly in which the FimC:FimF:FimG:FimH complex passes through FimD.
Geibel et al. (2013).
Geibel S, Procko E, Hultgren SJ, Baker D, & Waksman G (2013). Structural and energetic basis of folded-protein transport by the FimD usher.
Nature 496 :243-246.
PubMed Id: 23579681.
doi: 10.1038/nature12007.
Transferrin binding protein A (TbpA) in complex with human transferrin: Neisseria meningitidis serogroup b  B Bacteria (expressed in E. coli), 2.60 Å
TbpA in complex with human transferrin C-lobe, 3.10 Å: 3V89
Diferric human transferrin, 2.10 Å: 3V83
Apo-human transferrin C-lobe with bound sulfate ions, 1.70 Å: 3SKP
Transferrin binding protein B (TbpB), 2.40 Å: 3V8U
Noinaj et al. (2012).
Noinaj N, Easley NC, Oke M, Mizuno N, Gumbart J, Boura E, Steere AN, Zak O, Aisen P, Tajkhorshid E, Evans RW, Gorringe AR, Mason AB, Steven AC, & Buchanan SK (2012). Structural basis for iron piracy by pathogenic Neisseria.
Nature 483 :53-58.
PubMed Id: 22327295.
doi: 10.1038/nature10823.
Wzi outer-membrane lectin: Escherichia coli  B Bacteria, 2.64 Å
Assists in the formation of the bacterial capsule via direct interaction with capsular polysaccharides.
Bushell et al. (2013).
Bushell SR, Mainprize IL, Wear MA, Lou H, Whitfield C, & Naismith JH (2013). Wzi Is an Outer Membrane Lectin that Underpins Group 1 Capsule Assembly in Escherichia coli.
Structure 21 :844-853.
PubMed Id: 23623732.
doi: 10.1016/j.str.2013.03.010.
Opa60 for receptor-mediated engulfment, EXPLOR refined: Neisseria gonorrhoeae  B Bacteria, NMR strucuture
MD/EXPLOR refined structure, NMR structure: 2MAF
Fox et al. (2014).
Fox DA, Larsson P, Lo RH, Kroncke BM, Kasson PM, & Columbus L (2014). Structure of the neisserial outer membrane protein opa60: loop flexibility essential to receptor recognition and bacterial engulfment.
J Am Chem Soc 136 :9938-9946.
PubMed Id: 24813921.
doi: 10.1021/ja503093y.
CsgG bacterial amyloid secretion channel: Escherichia coli  B Bacteria, 3.59 Å
Pre-pore conformation, 2.80 Å: 4UV2
Goyal et al. (2014).
Goyal P, Krasteva PV, Van Gerven N, Gubellini F, Van den Broeck I, Troupiotis-Tsaïlaki A, Jonckheere W, Péhau-Arnaudet G, Pinkner JS, Chapman MR, Hultgren SJ, Howorka S, Fronzes R, & Remaut H (2014). Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG.
Nature 516 7530:250-253.
PubMed Id: 25219853.
doi: 10.1038/nature13768.
CsgG bacterial amyloid secretion channel: Escherichia coli  B Bacteria, 3.10 Å
Cao et al. (2014).
Cao B, Zhao Y, Kou Y, Ni D, Zhang XC, & Huang Y (2014). Structure of the nonameric bacterial amyloid secretion channel.
Proc Natl Acad Sci USA 111 50:E5439-E5444.
PubMed Id: 25453093.
doi: 10.1073/pnas.1411942111.
FusA plant-ferredoxin receptor: Pectobacterium atrosepticum  B Bacteria (expressed in E. coli), 3.2 Å
Grinter et al. (2016).
Grinter R, Josts I, Mosbahi K, Roszak AW, Cogdell RJ, Bonvin AM, Milner JJ, Kelly SM, Byron O, Smith BO, & Walker D (2016). Structure of the bacterial plant-ferredoxin receptor FusA.
Nat Commun 7 :13308.
PubMed Id: 27796364.
doi: 10.1038/ncomms13308.
Outer Membrane Autotransporters
NalP autotransporter translocator domain: Neisseria meningitidis  B Bacteria (expressed in E. coli), 2.60 Å
p6 122 space group. See also 1UYO, C222 1 space group, 3.2 Å resolution.
Oomen et al. (2004).
Oomen CJ, Van Ulsen P, Van Gelder P, Feijen M, Tommassen J, & Gros P (2004). Structure of the translocator domain of a bacterial autotransporter.
EMBO J 23 :1257-1266.
PubMed Id: 15014442.
Hia1022-1098 trimeric autotransporter: Haemophilus influenzae  B Bacteria (expressed in E. coli), 2.0 Å
Hia 992-1098, 2.3 Å: 2GR7
Meng et al. (2006).
Meng G, Surana NK, St Geme JW 3rd, Waksman G (2006). Structure of the outer membrane translocator domain of the Haemophilus influenzae Hia trimeric autotransporter.
EMBO J 25 :2297-2304.
PubMed Id: 16688217.
EspP autotransporter, post-cleavage state: Escherichia coli  B Bacteria, 2.7 Å
Barnard et al. (2007).
Barnard TJ, Dautin N, Lukacik P, Bernstein HD, & Buchanan SK (2007). Autotransporter structure reveals intra-barrel cleavage followed by conformational changes.
Nature Struc Mol Biol 14 :1214-1220.
PubMed Id: 17994105.
EspP autotransporter, pre-cleavage state (N1023A mutant): Escherichia coli  B Bacteria, 2.48 Å
Pre-cleavage structure (N1023D mutant), 2.52 Å: 3SLO
Pre-cleavage structure (N1023S mutant), 2.46 Å: 3SLT
Barnard et al. (2012).
Barnard TJ, Gumbart J, Peterson JH, Noinaj N, Easley NC, Dautin N, Kuszak AJ, Tajkhorshid E, Bernstein HD, & Buchanan SK (2012). Molecular Basis for the Activation of a Catalytic Asparagine Residue in a Self-Cleaving Bacterial Autotransporter.
J Mol Biol 415 :128-142.
PubMed Id: 22094314.
doi: 10.1016/j.jmb.2011.10.049.
EspP autotransporter passenger domain: Escherichia coli  B Bacteria, 2.50 Å
Like a number of other auto-cleaved passengers, a parallel β-helix is a characteristic feature.
Khan et al. (2011).
Khan S, Mian HS, Sandercock LE, Chirgadze NY, & Pai EF (2011). Crystal Structure of the Passenger Domain of the Escherichia coli Autotransporter EspP.
J Mol Biol 413 :985-1000.
PubMed Id: 21964244.
doi: 10.1016/j.jmb.2011.09.028.
Hbp (hemoglobin protease) self-cleaving autotransporter with truncated passenger: Escherichia coli  B Bacteria, 2.00 Å
The structure shows the pre-cleavage state.
Tajima et al. (2010).
Tajima N, Kawai F, Park SY, & Tame JR (2010). A novel intein-like autoproteolytic mechanism in autotransporter proteins.
J Mol Biol 402 :645-656.
PubMed Id: 20615416.
doi: 10.1016/j.jmb.2010.06.068.
Hbp (hemoglobin protease) full-length passenger domain: Escherichia coli  B Bacteria, 2.20 Å
The passenger domain has a prominent β-helix domain.
Otto et al. (2005).
Otto BR, Sijbrandi R, Luirink J, Oudega B, Heddle JG, Mizutani K, Park SY, & Tame JR (2005). Crystal structure of hemoglobin protease, a heme binding autotransporter protein from pathogenic Escherichia coli.
J Biol Chem 280 :17339-17345.
PubMed Id: 15728184.
doi: 10.1074/jbc.M412885200.
EstA Autotransporter, full length: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), 2.50 Å
This is the first full-length structure of an autotransporter. The passenger is not cleaved physiologically, but rather presents an esterase domain to the external world.
van den Berg (2010).
van den Berg B (2010). Crystal Structure of a Full-Length Autotransporter.
J Mol Biol 396 :627-633.
PubMed Id: 20060837.
IcsA autotransporter (autochaperone region only): Shigella flexneri  B Bacteria (expressed in E. coli), 2.00 Å
Kühnel & Diezmann (2011).
Kühnel K & Diezmann D (2011). Crystal structure of the autochaperone region from the Shigella flexneri autotransporter IcsA.
J Bacteriol 193 :2042-2045 .
PubMed Id: 21335457.
doi: 10.1128/JB.00790-10.
Intimin outer membrane β-domain: Escherichia coli  B Bacteria, 1.86 Å
The C-terminal passenger domain, not present in this structure, is involved in adhesion to host cells.
Fairman et al. (2012).
Fairman JW, Dautin N, Wojtowicz D, Liu W, Noinaj N, Barnard TJ, Udho E, Przytycka TM, Cherezov V, & Buchanan SK (2012). Crystal structures of the outer membrane domain of intimin and invasin from enterohemorrhagic E. coli and enteropathogenic Y. pseudotuberculosis.
Structure 20 :1233-1243.
PubMed Id: 22658748.
doi: 10.1016/j.str.2012.04.011.
Intimin C-terminal passenger domain in complex with receptor: Escherichia coli  B Bacteria, 2.90 Å
Luo et al. (2000).
Luo Y, Frey EA, Pfuetzner RA, Creagh AL, Knoechel DG, Haynes CA, Finlay BB, & Strynadka NC (2000). Crystal structure of enteropathogenic Escherichia coli intimin-receptor complex.
Nature 405 :1073-1077.
PubMed Id: 10890451.
doi: 10.1038/35016618.


See also:
Batchelor et al. (2000).
Batchelor M, Prasannan S, Daniell S, Reece S, Connerton I, Bloomberg G, Dougan G, Frankel G, & Matthews S (2000). Structural basis for recognition of the translocated intimin receptor (Tir) by intimin from enteropathogenic Escherichia coli.
EMBO J 19 :2452-2464.
PubMed Id: 10835344.
Invasin outer membrane β-domain: Yersinia pseudotuberculosis  B Bacteria (expressed in E. coli), 2.26 Å
The C-terminal passenger domain, not present in this structure, is involved in adhesion to host cells.
Fairman et al. (2012).
Fairman JW, Dautin N, Wojtowicz D, Liu W, Noinaj N, Barnard TJ, Udho E, Przytycka TM, Cherezov V, & Buchanan SK (2012). Crystal structures of the outer membrane domain of intimin and invasin from enterohemorrhagic E. coli and enteropathogenic Y. pseudotuberculosis.
Structure 20 :1233-1243.
PubMed Id: 22658748.
doi: 10.1016/j.str.2012.04.011.
Invasin C-terminal passenger domain: Yersinia pseudotuberculosis  B Bacteria (expressed in E. coli), 2.30 Å
Hamburger et al. (1999).
Hamburger ZA, Brown MS, Isberg RR, & Bjorkman PJ (1999). Crystal structure of invasin: a bacterial integrin-binding protein.
Science 286 :291-295.
PubMed Id: 10514372.
YadA trimeric adhesin autotransporter: Yersinia enterocolitica subsp. enterocolitica 8081  B Bacteria (expressed in E. coli), NMR Structure
Structure determined from microcrystals using solid-state NMR
Shahid et al. (2012).
Shahid SA, Bardiaux B, Franks WT, Krabben L, Habeck M, van Rossum BJ, & Linke D (2012). Membrane-protein structure determination by solid-state NMR spectroscopy of microcrystals.
Nature Methods 9 :1212-1217.
PubMed Id: 23142870.
TamA Autotransporter, full length: Escherichia coli  B Bacteria, 2.25 Å
TamA POTRA domains 1-3, 1.84 Å: 4BZA
Gruss et al. (2013).
Gruss F, Zähringer F, Jakob RP, Burmann BM, Hiller S, & Maier T (2013). The structural basis of autotransporter translocation by TamA.
Nat Struct Mol Biol 20 :1318-1320.
PubMed Id: 24056943.
doi: 10.1038/nsmb.2689.
TibC dodecameric glycosyltransferase (type V secretion system): Escherichia coli ETEC H10407  B Bacteria (expressed in E. coli), 2.88 Å
in complex with ADP-D-beta-D-heptose, 3.88 Å: 4RB4

Cryo-EM structures of the TibC 12-TibA 6 are available in the EM Databank with accession numbers EMD-2755, -2756, -2757, and -2758.
Yao et al. (2014).
Yao Q, Lu Q, Wan X, Song F, Xu Y, Hu M, Zamyatina A, Liu X, Huang N, Zhu P, & Shao F (2014). A structural mechanism for bacterial autotransporter glycosylation by a dodecameric heptosyltransferase family.
Elife 3 .
PubMed Id: 25310236.
doi: 10.7554/eLife.03714.
Omp85-TpsB Outer Membrane Transporter Superfamily
FhaC Filamentous Hemagglutinin Transporter: Bordetella pertussis  B Bacteria (expressed in E. coli), 3.15 Å
The first outer membrane protein from the Omp85–two-partner secretion B (TpsB) superfamily. Supersedes 2QDZ.
Clantin et al. (2007).
Clantin B, Delattre AS, Rucktooa P, Saint N, Meli AC, Locht C, Jacob-Dubuisson F, & Villeret V (2007). Structure of the membrane protein FhaC: a member of the Omp85-TpsB transporter superfamily.
Science 317 :957-961.
PubMed Id: 17702945.
FhaC Filamentous Hemagglutinin Transporter, R450A mutant: Bordetella pertussis  B Bacteria (expressed in E. coli), 3.50 Å
Delattre et al. (2010).
Delattre AS, Clantin B, Saint N, Locht C, Villeret V, & Jacob-Dubuisson F (2010). Functional importance of a conserved sequence motif in FhaC, a prototypic member of the TpsB/Omp85 superfamily.
FEBS J 277 :4755-4765.
PubMed Id: 20955520.
doi: 10.1111/j.1742-4658.2010.07881.x.
TeOmp85-N POTRA domains: Thermosynechococcus elongatus  B Bacteria (expressed in E. coli), 1.97 Å
Structure is of complete N-terminus containing three POTRA domains. The polypeptide transport-associated (POTRA) domains link to a transmembrane β-barrel, which is absent in this structure.
Arnold et al. (2010).
Arnold T, Zeth K, & Linke D (2010). Omp85 from the thermophilic cyanobacterium thermosynechococcus elongatus differs from proteobacterial Omp85 in structure and domain composition.
J Biol Chem 285 :18003-18015.
PubMed Id: 20351097.
anaOmp85-N POTRA domains (hexagonal crystals): Anabaena sp. PCC7120  B Bacteria (expressed in E. coli), 2.20 Å
Structure is of complete N-terminus containing three POTRA domains. The polypeptide transport-associated (POTRA) domains link to a transmembrane β-barrel, which is absent in this structure.
Tetragonal crystals, 2.59 Å: 3MC8
Koenig et al. (2010).
Koenig P, Mirus O, Haarmann R, Sommer M, Sinning I, Schleiff E, & Tews I (2010). Conserved properties of POTRA domains derived from cyanobacterial OMP85.
J Biol Chem 285 :18016-18024.
PubMed Id: 20348103.
BamA with POTRA domains 1 - 5: Neisseria gonorrhoeae  B Bacteria (expressed in E. coli), 3.20 Å
This is the full-length BamA structure.
Noinaj et al. (2013).
Noinaj N, Kuszak AJ, Gumbart JC, Lukacik P, Chang H, Easley NC, Lithgow T, & Buchanan SK (2013). Structural insight into the biogenesis of β-barrel membrane proteins.
Nature 501 :385-390.
PubMed Id: 23995689.
doi: 10.1038/nature12521.
BamA with POTRA domains 4 & 5: Haemophilus ducreyi  B Bacteria (expressed in E. coli), 2.91 Å
Noinaj et al. (2013).
Noinaj N, Kuszak AJ, Gumbart JC, Lukacik P, Chang H, Easley NC, Lithgow T, & Buchanan SK (2013). Structural insight into the biogenesis of β-barrel membrane proteins.
Nature 501 :385-390.
PubMed Id: 23995689.
doi: 10.1038/nature12521.
BamA with POTRA domain 5: Escherichia coli  B Bacteria, 3.00 Å
Albrecht et al. (2014).
Albrecht R, Schütz M, Oberhettinger P, Faulstich M, Bermejo I, Rudel T, Diederichs K, & Zeth K (2014). Structure of BamA, an essential factor in outer membrane protein biogenesis.
Acta Crystallogr D Biol Crystallogr 70 :1779-1789.
PubMed Id: 24914988.
doi: 10.1107/S1399004714007482.
BamA21-351 POTRA domains (periplasmic fragment, P212121): Escherichia coli  B Bacteria, 2.2 Å
BamA was formerly named YaeT. The polypeptide transport-associated (POTRA) domains link to a transmembrane β-barrel, which is absent in this structure.
P2 12 12 space group, 2.2 Å: 2QDF
Kim et al. (2007).
Kim S, Malinverni JC, Sliz P, Silhavy TJ, Harrison SC, & Kahne D (2007). Structure and function of an essential component of the outer membrane protein assembly machine.
Science 317 :961-964.
PubMed Id: 17702946.
BamA21-410 POTRA domains (periplasmic fragment): Escherichia coli  B Bacteria, 3.3 Å
BamA was formerly named YaeT. The polypeptide transport-associated (POTRA) domains link to a transmembrane β-barrel, which is absent in this structure. Structure shows the first four POTRA domains in an extended conformation.
Gatzeva-Topalova et al. (2008).
Gatzeva-Topalova PZ, Walton TA, & Sousa MC (2008). Crystal Structure of YaeT: Conformational flexibility and substrate recognition.
Structure 16 :1873-1881.
PubMed Id: 19081063.
BamA21-174 POTRA domains 1 and 2: Escherichia coli  B Bacteria, NMR Structure
BamA was formerly named YaeT.
Knowles et al. (2008).
Knowles TJ, Jeeves M, Bobat S, Dancea F, McClelland D, Palmer T, Overduin M, & Henderson IR (2008). Fold and function of polypeptide transport-associated domains responsible for delivering unfolded proteins to membranes.
Mol Microbiol 68 :1216-1227.
PubMed Id: 18430136.
BamA264-424 POTRA domains 4 and 5: Escherichia coli  B Bacteria, 2.69 Å
BamA was formerly named YaeT. From this structure and earlier ones (above), Gatzeva-Topalova et al. have constructed a 'spliced' model for the complete POTRA1-5 structure.
Gatzeva-Topalova et al. (2010).
Gatzeva-Topalova PZ, Warner LR, Pardi A, & Sousa MC (2010). Structure and Flexibility of the Complete Periplasmic Domain of BamA: The Protein Insertion Machine of the Outer Membrane.
Structure 18 :1492-1501.
PubMed Id: 21070948.
BamA266-420 POTRA domains 4 and 5: Escherichia coli  B Bacteria, 1.5 Å
BamA formerly named YaeT.
Zhang et al. (2011).
Zhang H, Gao ZQ, Hou HF, Xu JH, Li LF, Su XD, & Dong YH (2011). High-resolution structure of a new crystal form of BamA POTRA4-5 from Escherichia coli.
Acta Crystallogr Sect F Struct Biol Cryst Commun F67 :734-738.
PubMed Id: 21795783.
doi: 10.1107/S1744309111014254.
BamB component of the Bam β-barrel assembly machine: Escherichia coli  B Bacteria, 1.80 Å
Heuck et al. (2011).
Heuck A, Schleiffer A, & Clausen T (2011). Augmenting β-Augmentation: Structural Basis of How BamB Binds BamA and May Support Folding of Outer Membrane Proteins.
J Mol Biol 406 :659-666.
PubMed Id: 21236263.
BamB component of the Bam β-barrel assembly machine: Escherichia coli  B Bacteria, 2.60 Å
Kim & Paetzel (2011).
Kim KH & Paetzel M (2011). Crystal Structure of Escherichia coli BamB, a Lipoprotein Component of the β-Barrel Assembly Machinery Complex.
J Mol Biol 406 :667-678.
PubMed Id: 21168416.
BamB component of the Bam β-barrel assembly machine, I222 space group: Escherichia coli  B Bacteria, 1.65 Å
P2 12 12 1 space group, 1.77 Å: 3Q7N
P2 13 space group, 2.09 Å: 3Q7O
Noinaj et al. (2011).
Noinaj N, Fairman JW, & Buchanan SK (2011). Crystal structures The Crystal Structure of BamB Suggests Interactions with BamA and Its Role within the BAM Complex.
J Mol Biol 407 :248-260.
PubMed Id: 21277859.
BamB component of the Bam β-barrel assembly machine: Escherichia coli  B Bacteria, 2.60 Å
Albrecht & Zeth (2011).
Albrecht R & Zeth K (2011). Structural basis of outer membrane protein biogenesis in bacteria.
J Biol Chem 286 :27792-27803.
PubMed Id: 21586578.
doi: 10.1074/jbc.M111.238931.
BamB component of the Bam β-barrel assembly machine: Escherichia coli  B Bacteria, 2.00 Å
Dong et al. (2012).
Dong C, Yang X, Hou HF, Shen YQ, & Dong YH (2012). Structure of Escherichia coli BamB and its interaction with POTRA domains of BamA.
Acta Crystallogr D Biol Crystallogr D68 :1134-1139.
PubMed Id: 22948914.
doi: 10.1107/S0907444912023141.
BamB in complex with POTRA 3-4 domains of BamA: Escherichia coli  B Bacteria, 2.15 Å
Chen et al. (2016).
Chen Z, Zhan LH, Hou HF, Gao ZQ, Xu JH, Dong C, & Dong YH (2016). Structural basis for the interaction of BamB with the POTRA3-4 domains of BamA.
Acta Crystallogr D Struct Biol 72 :236-244.
PubMed Id: 26894671.
doi: 10.1107/S2059798315024729.
BamC component of the Bam β-barrel assembly machine: Escherichia coli  B Bacteria, 1.55 Å
C-terminal domain, residues 101-212
Albrecht & Zeth (2011).
Albrecht R & Zeth K (2011). Structural basis of outer membrane protein biogenesis in bacteria.
J Biol Chem 286 :27792-27803.
PubMed Id: 21586578.
doi: 10.1074/jbc.M111.238931.
BamC component of the Bam β-barrel assembly machine: Escherichia coli  B Bacteria, 1.25 Å
N-terminal domain, residues 25-143
Albrecht & Zeth (2011).
Albrecht R & Zeth K (2011). Structural basis of outer membrane protein biogenesis in bacteria.
J Biol Chem 286 :27792-27803.
PubMed Id: 21586578.
doi: 10.1074/jbc.M111.238931.
BamC component of the Bam β-barrel assembly machine (N-term, 101-212): Escherichia coli  B Bacteria, NMR Structure
Structure obtained Using Rosetta with a limited NMR data set.
C-term domain, 229-344: 2LAE
Warner et al. (2011).
Warner LR, Varga K, Lange OF, Baker SL, Baker D, Sousa MC, & Pardi A (2011). Structure of the BamC two-domain protein obtained by Rosetta with a limited NMR data set.
J Mol Biol 411 :83-95.
PubMed Id: 21624375.
doi: 10.1016/j.jmb.2011.05.022.
BamC component of the Bam β-barrel assembly machine (C-term, 224-343): Escherichia coli  B Bacteria, 1.50 Å
Kim et al. (2011).
Kim KH, Aulakh S, Tan W, & Paetzel M (2011). Crystallographic analysis of the C-terminal domain of the Escherichia coli lipoprotein BamC.
Acta Crystallogr Sect F Struct Biol Cryst Commun 67 :1350-1358.
PubMed Id: 22102230.
doi: 10.1107/S174430911103363X.
BamD component of the Bam β-barrel assembly machine: Rhodothermus marinus  B Bacteria (expressed in E. coli), 2.15 Å
BamD associates with the membrane using a lipidated amino-terminal cysteine. BamE and BamC are thought to bind to the C-terminus of BamD.
Sandoval et al. (2011).
Sandoval CM, Baker SL, Jansen K, Metzner SI, & Sousa MC (2011). Crystal Structure of BamD: An Essential Component of the β-Barrel Assembly Machinery of Gram-Negative Bacteria
J Mol Biol 409 :348-357.
PubMed Id: 21463635.
doi: 10.1016/j.jmb.2011.03.035.
BamD component of the Bam β-barrel assembly machine: Escherichia coli  B Bacteria, 1.80 Å
Albrecht & Zeth (2011).
Albrecht R & Zeth K (2011). Structural basis of outer membrane protein biogenesis in bacteria.
J Biol Chem 286 :27792-27803.
PubMed Id: 21586578.
doi: 10.1074/jbc.M111.238931.
BamD component of the Bam β-barrel assembly machine: Escherichia coli  B Bacteria, 2.60 Å
Dong et al. (2012).
Dong C, Hou HF, Yang X, Shen YQ, & Dong YH (2012). Structure of Escherichia coli BamD and its functional implications in outer membrane protein assembly.
Acta Crystallogr D68 :95-101.
PubMed Id: 22281737.
doi: 10.1107/S0907444911051031.
BamD component of the Bam β-barrel assembly machine: Neisseria gonorrhoeae  B Bacteria (expressed in E. coli), 2.50 Å
Sikora et al. (2018).
Sikora AE, Wierzbicki IH, Zielke RA, Ryner RF, Korotkov KV, Buchanan SK, & Noinaj N (2018). Structural and functional insights into the role of BamD and BamE within the ?-barrel assembly machinery in Neisseria gonorrhoeae.
J Biol Chem 293 :1106-1119.
PubMed Id: 29229778.
doi: 10.1074/jbc.RA117.000437.
BamE component of the Bam β-barrel assembly machine: Escherichia coli  B Bacteria, NMR structure
Knowles et al. (2011).
Knowles TJ, Browning DF, Jeeves M, Maderbocus R, Rajesh S, Sridhar P, Manoli E, Emery D, Sommer U, Spencer A, Leyton DL, Squire D, Chaudhuri RR, Viant MR, Cunningham AF, Henderson IR, Overduin M (2011). Structure and function of BamE within the outer membrane and the β-barrel assembly machine.
EMBO Rep 12 :123-128.
PubMed Id: 21212804.
BamE component of the Bam β-barrel assembly machine: Escherichia coli  B Bacteria, 1.80 Å
Albrecht & Zeth (2011).
Albrecht R & Zeth K (2011). Structural basis of outer membrane protein biogenesis in bacteria.
J Biol Chem 286 :27792-27803.
PubMed Id: 21586578.
doi: 10.1074/jbc.M111.238931.
BamE component of the Bam β-barrel assembly machine: Neisseria gonorrhoeae  B Bacteria (expressed in E. coli), 2.45 Å
Sikora et al. (2018).
Sikora AE, Wierzbicki IH, Zielke RA, Ryner RF, Korotkov KV, Buchanan SK, & Noinaj N (2018). Structural and functional insights into the role of BamD and BamE within the ?-barrel assembly machinery in Neisseria gonorrhoeae.
J Biol Chem 293 :1106-1119.
PubMed Id: 29229778.
doi: 10.1074/jbc.RA117.000437.
BamCD complex of the Bam β-barrel assembly machine: Escherichia coli  B Bacteria, 2.90 Å
The BamC component is the N-terminal domain, residues 26-217. The BamD component includes residues 32-240.
Kim et al. (2011).
Kim KH, Aulakh S, & Paetzel M (2011). Crystal Structure of β-Barrel Assembly Machinery BamCD Protein Complex
J Biol Chem 286 :39116-39121.
PubMed Id: 21937441.
doi: 10.1074/jbc.M111.298166.
BamACDE complex of the Bam β-barrel assembly machine: Escherichia coli  B Bacteria, 3.4 Å
Bakelar et al. (2016).
Bakelar J, Buchanan SK, & Noinaj N (2016). The structure of the β-barrel assembly machinery complex.
Science 351 :180-186.
PubMed Id: 26744406.
doi: 10.1126/science.aad3460.
BamA-POTRA4-5-BamD fusion complex of the Bam β-barrel assembly machine: Rhodothermus marinus  B Bacteria (expressed in E. coli), 2.0 Å
Bergal et al. (2016).
Bergal HT, Hopkins AH, Metzner SI, & Sousa MC (2016). The Structure of a BamA-BamD Fusion Illuminates the Architecture of the β-Barrel Assembly Machine Core.
Structure 24 :243-251.
PubMed Id: 26749448.
doi: 10.1016/j.str.2015.10.030.
BamABCDE complex of the Bam β-barrel assembly machine: Escherichia coli  B Bacteria, 2.90 Å
BAM ACDE complex, 3.90 Å: 5D0Q
Gu et al. (2016).
Gu Y, Li H, Dong H, Zeng Y, Zhang Z, Paterson NG, Stansfeld PJ, Wang Z, Zhang Y, Wang W, & Dong C (2016). Structural basis of outer membrane protein insertion by the BAM complex.
Nature 531 :64-69.
PubMed Id: 26901871.
doi: 10.1038/nature17199.
BamABCDE complex of the Bam β-barrel assembly machine: Escherichia coli  B Bacteria, 3.56 Å
Han et al. (2016).
Han L, Zheng J, Wang Y, Yang X, Liu Y, Sun C, Cao B, Zhou H, Ni D, Lou J, Zhao Y, & Huang Y (2016). Structure of the BAM complex and its implications for biogenesis of outer-membrane proteins.
Nat Struct Mol Biol 23 :192-196.
PubMed Id: 26900875.
doi: 10.1038/nsmb.3181.
BamABCDE complex of the Bam β-barrel assembly machine: Escherichia coli  B Bacteria, 4.9 Å
cryo-EM structure showing lateral opening of complex
Iadanza et al. (2016).
Iadanza MG, Higgins AJ, Schiffrin B, Calabrese AN, Brockwell DJ, Ashcroft AE, Radford SE, & Ranson NA (2016). Lateral opening in the intact β-barrel assembly machinery captured by cryo-EM.
Nat Commun 7 :12865.
PubMed Id: 27686148.
doi: 10.1038/ncomms12865.
Beta-Barrel Membrane Proteins: Mitochondrial Outer Membrane
VDAC-1 voltage dependent anion channel: Homo sapiens  E Eukaryota (expressed in E. coli), NMR structure
Structure determined in LDAO micelles.
Hiller et al. (2008).
Hiller S, Garces RG, Malia TJ, Orekhov VY, Colombini M, & Wagner G (2008). Solution structure of the integral human membrane protein VDAC-1 in detergent micelles.
Science 321 :1206-1210.
PubMed Id: 18755977.
VDAC-1 voltage dependent anion channel: Homo sapiens  E Eukaryota (expressed in E. coli), 4 Å
Structure determined by combining x-ray and NMR data.
Bayrhuber et al. (2008).
Bayrhuber M, Meins T, Habeck M, Becker S, Giller K, Villinger S, Vonrhein C, Griesinger C, Zweckstetter M, & Zeth K (2008). Structure of the human voltage-dependent anion channel.
Proc Natl Acad Sci USA 105 :15370-15375.
PubMed Id: 18832158.
VDAC-1 voltage dependent anion channel: Mus musculus  E Eukaryota (expressed in E. coli), 2.3 Å
Reveals the voltage-sensing N-terminal α-helix.
Ujwal et al. (2008).
Ujwal R, Cascio D, Colletier JP, Faham S, Zhang J, Toro L, Ping P, & Abramson J (2008). The crystal structure of mouse VDAC1 at 2.3 Å resolution reveals mechanistic insights into metabolite gating.
Proc Natl Acad Sci USA 105 :17742-17747.
PubMed Id: 18988731.
VDAC-1 voltage dependent anion channel with bound ATP: Mus musculus  E Eukaryota (expressed in E. coli), 2.28 Å
Choudhary et al. (2014).
Choudhary OP, Paz A, Adelman JL, Colletier JP, Abramson J, & Grabe M (2014). Structure-guided simulations illuminate the mechanism of ATP transport through VDAC1.
Nat Struct Mol Biol 21 7:626-632.
PubMed Id: 24908397.
doi: 10.1038/nsmb.2841.
VDAC-2 voltage dependent anion channel: Danio rerio  E Eukaryota (expressed in E. coli), 2.80 Å
Double electron-electron resonance measurements indicate a population of oligomers.
Schredelseker et al. (2014).
Schredelseker J, Paz A, López CJ, Altenbach C, Leung CS, Drexler MK, Chen JN, Hubbell WL, & Abramson J (2014). High-Resolution Structure and Double Electron-Electron Resonance of the Zebrafish Voltage Dependent Anion Channel 2 Reveal an Oligomeric Population.
J Biol Chem 289 :12566-12577.
PubMed Id: 24627492.
doi: 10.1074/jbc.M113.497438.
Translocase of outer mitochondrial membrane (TOM) complex, model: Neurospora crassa  E Eukaryota, 6.8 Å
single-particle cryo-EM structure
Bausewein et al. (2017).
Bausewein T, Mills DJ, Langer JD, Nitschke B, Nussberger S, & Kühlbrandt W (2017). Cryo-EM Structure of the TOM Core Complex from Neurospora crassa.
Cell 170 :693-700.e7.
PubMed Id: 28802041.
doi: 10.1016/j.cell.2017.07.012.
Lipopolysaccharide (LPS) Transport Proteins
LptD-LptE lipopolysaccharide transport complex: Salmonella enterica  B Bacteria (expressed in E. coli), 2.80 Å
Structure provides the basis for LPS translocation across the outer membrane. LptD comprises residues 226-786. LptE comprises residues 19 - 169.
Dong et al. (2014).
Dong H, Xiang Q, Gu Y, Wang Z, Paterson NG, Stansfeld PJ, He C, Zhang Y, Wang W, & Dong C (2014). Structural basis for outer membrane lipopolysaccharide insertion.
Nature 511 :52-56.
PubMed Id: 24990744.
doi: 10.1038/nature13464.
LptD-LptE lipopolysaccharide transport complex: Shigella flexneri  B Bacteria (expressed in E. coli), 2.39 Å
Qiao et al. (2014).
Qiao S, Luo Q, Zhao Y, Zhang XC, & Huang Y (2014). Structural basis for lipopolysaccharide insertion in the bacterial outer membrane.
Nature 511 :108-111.
PubMed Id: 24990751.
doi: 10.1038/nature13484.
LptE lipopolysaccharide transport protein: Escherichia coli  B Bacteria, 2.34 Å
Malojčić et al. (2014).
Malojčić G, Andres D, Grabowicz M, George AH, Ruiz N, Silhavy TJ, & Kahne D (2014). LptE binds to and alters the physical state of LPS to catalyze its assembly at the cell surface.
Proc. Natl. Acad. Sci. U.S.A. 111 26:9467-9472.
PubMed Id: 24938785.
doi: 10.1073/pnas.1402746111.
LptD-LptE lipopolysaccharide transport complex: Yersinia pestis  B Bacteria (expressed in E. coli), 2.75 Å
Botos et al. (2016).
Botos I, Majdalani N, Mayclin SJ, McCarthy JG, Lundquist K, Wojtowicz D, Barnard TJ, Gumbart JC, & Buchanan SK (2016). Structural and Functional Characterization of the LPS Transporter LptDE from Gram-Negative Pathogens.
Structure 24 :965-976.
PubMed Id: 27161977.
doi: 10.1016/j.str.2016.03.026.
LptD-LptE lipopolysaccharide transport complex: Klebsiella pneumoniae  B Bacteria (expressed in E. coli), 2.94 Å
full-length protein, 4.37 Å: 5IV9
Botos et al. (2016).
Botos I, Majdalani N, Mayclin SJ, McCarthy JG, Lundquist K, Wojtowicz D, Barnard TJ, Gumbart JC, & Buchanan SK (2016). Structural and Functional Characterization of the LPS Transporter LptDE from Gram-Negative Pathogens.
Structure 24 :965-976.
PubMed Id: 27161977.
doi: 10.1016/j.str.2016.03.026.
LptD-LptE lipopolysaccharide transport complex: Pseudomonas aeruginosa  B Bacteria (expressed in E. coli), 2.99 Å
Botos et al. (2016).
Botos I, Majdalani N, Mayclin SJ, McCarthy JG, Lundquist K, Wojtowicz D, Barnard TJ, Gumbart JC, & Buchanan SK (2016). Structural and Functional Characterization of the LPS Transporter LptDE from Gram-Negative Pathogens.
Structure 24 :965-976.
PubMed Id: 27161977.
doi: 10.1016/j.str.2016.03.026.
Polysaccharide Utilization Proteins
Genes of this family are part of the starch utilization system (SUS)
SusCD complex BT2261-2264, space group P1: Bacteroides thetaiotaomicron  B Bacteria, 2.75 Å
Space group P2 12 12 1, 3.4 Å: 5QF7
Space group P2 1, 2.8 Å: 5FQ6
BT2262 complex, 3.1 Å: 5QF3
BT2263 complex, 1.9 Å: 5FQ4
BT1762, 1.76 Å: 5LX8
BT1762-1763, 3.1 Å: 5T3R
BT1762-1763, 3.1 Å: 5T4Y
Glenwright et al. (2017).
Glenwright AJ, Pothula KR, Bhamidimarri SP, Chorev DS, Baslé A, Firbank SJ, Zheng H, Robinson CV, Winterhalter M, Kleinekathöfer U, Bolam DN, & van den Berg B (2017). Structural basis for nutrient acquisition by dominant members of the human gut microbiota.
Nature 541 7637:407-411.
PubMed Id: 28077872.
doi: 10.1038/nature20828.
Type II Secretion Systems
GspD secretin: Escherichia coli  B Bacteria, 3.04 Å
cryo-EM structure
Yan et al. (2017).
Yan Z, Yin M, Xu D, Zhu Y, & Li X (2017). Structural insights into the secretin translocation channel in the type II secretion system.
Nat Struct Mol Biol 24 :177-183.
PubMed Id: 28067918.
doi: 10.1038/nsmb.3350.
GspD secretin: Vibrio cholerae  B Bacteria (expressed in E. coli), 3.26 Å
cryo-EM structure
partially open state without the cap gate, 4.22 Å: 5WQ9
Yan et al. (2017).
Yan Z, Yin M, Xu D, Zhu Y, & Li X (2017). Structural insights into the secretin translocation channel in the type II secretion system.
Nat Struct Mol Biol 24 :177-183.
PubMed Id: 28067918.
doi: 10.1038/nsmb.3350.
Type III Secretion Systems
TS3 injectisome basal body: Salmonella enterica  B Bacteria, 6.3 Å
cryo-EM structure
periplasmic domains of PrgH and PrgK, 4.3 Å: 5TCP
secretin InvG, 3.6 Å: 5TCQ
Worrall et al. (2016).
Worrall LJ, Hong C, Vuckovic M, Deng W, Bergeron JR, Majewski DD, Huang RK, Spreter T, Finlay BB, Yu Z, & Strynadka NC (2016). Near-atomic-resolution cryo-EM analysis of the Salmonella T3S injectisome basal body.
Nature 540 :597-601.
PubMed Id: 27974800.
doi: 10.1038/nature20576.
Adventitious Membrane Proteins: Beta-sheet Pore-forming Toxins/Attack Complexes
α-hemolysin: Staphylococcus aureus  B Bacteria, 1.9 Å
Song et al. (1996).
Song L, Hobaugh MR, Shustak C, Cheley S, Bayley H, & Gouaux JE (1996). Structure of staphylococcal a -hemolysin, a heptameric transmembrane pore.
Science 274 :1859-1866.
PubMed Id: 8943190.
α-hemolysin, M113F mutant: Staphylococcus aureus  B Bacteria, 2.10 Å
M113F mutant complexed with β-cyclodextrin, 2.20 Å: 3M3R
M113N mutant, 1.90 Å: 3M4D
M113N mutant complexed with β-cyclodextrin, 2.30 Å: 3M4E
Banerjee et al. (2010).
Banerjee A, Mikhailova E, Cheley S, Gu LQ, Montoya M, Nagaoka Y, Gouaux E, & Bayley H (2010). Molecular bases of cyclodextrin adapter interactions with engineered protein nanopores.
Proc Natl Acad Sci USA 107 :8165-8170.
PubMed Id: 20400691.
doi: 10.1073/pnas.0914229107 .
α-hemolysin: Staphylococcus aureus  B Bacteria (expressed in E. coli), 2.30 Å
Crystals were prepared using 2-methyl-2,4-pentanediol without detergent.
Tanaka et al. (2011).
Tanaka Y, Hirano N, Kaneko J, Kamio Y, Yao M, & Tanaka I (2011). 2-Methyl-2,4-pentanediol induces spontaneous assembly of staphylococcal α-hemolysin into heptameric pore structure.
Protein Sci 20 :448-456.
PubMed Id: 21280135.
doi: 10.1002/pro.579.
γ-hemolysin composed of LukF and Hlg2: Staphylococcus aureus  B Bacteria (expressed in E. coli), 2.50 Å
Yamashita et al. (2011).
Yamashita K, Kawai Y, Tanaka Y, Hirano N, Kaneko J, Tomita N, Ohta M, Kamio Y, Yao M, & Tanaka I (2011). Crystal structure of the octameric pore of staphylococcal γ-hemolysin reveals the β-barrel pore formation mechanism by two components.
Proc Natl Acad Sci USA 108 :17314-17319.
PubMed Id: 21969538.
doi: 10.1073/pnas.1110402108.
γ-hemolysin prepore: Staphylococcus aureus  B Bacteria (expressed in E. coli), 2.99 Å
Yamashita et al. (2014).
Yamashita D, Sugawara T, Takeshita M, Kaneko J, Kamio Y, Tanaka I, Tanaka Y, & Yao M (2014). Molecular basis of transmembrane beta-barrel formation of staphylococcal pore-forming toxins.
Nat Commun 5 :4897.
PubMed Id: 25263813.
doi: 10.1038/ncomms5897.
LukF component of γ-hemolysin: Staphylococcus aureus  B Bacteria (expressed in E. coli), 1.9 Å
The structure is of the water soluble form of the protein.
At 2.5 Å: 2LKF. With bound phosphocholine, 1.9 Å: 3LKF
Olson et al. (1999).
Olson R, Nariya H, Yokota K, Kamio Y, & Gouaux E (1999). Crystal structure of Staphylococcal LukF delineates conformational changes accompanying formation of a transmembrane channel.
Nature Struc. Biol 6 :134-140.
PubMed Id: 10048924.
LUK prepore formed from LukF & LukS: Staphylococcus aureus  B Bacteria (expressed in E. coli), 2.40 Å
Yamashita et al. (2014).
Yamashita D, Sugawara T, Takeshita M, Kaneko J, Kamio Y, Tanaka I, Tanaka Y, & Yao M (2014). Molecular basis of transmembrane beta-barrel formation of staphylococcal pore-forming toxins.
Nat Commun 5 :4897.
PubMed Id: 25263813.
doi: 10.1038/ncomms5897.
Perfringolysin O (PFO) protomer: Clostridium perfringens  B Bacteria (expressed in E. coli), 2.20 Å
The protein is a thiol-activated cytolysin that uses membrane cholesterol as a receptor.
40 or more protomers assemble into a large pore anchored in the bilayer by the β-sheets of
domain 4. Space group is C222 1. P2 12 12 space group, 3.0 Å: 1M3J. P3 1 space group, 2.90 Å: 1M3I.
Rossjohn et al. (1997).
Rossjohn J, Feil SC, McKinstry WJ, Tweten RK, & Parker MW (1997). Structure of a cholesterol-binding, thiol-activated cytolysin and a model of its membrane form.
Cell 89 :685-692.
PubMed Id: 9182756.
Anthrax Protective Antigen (PA) and Lethal Factor (LF) Prechannel Complex: Bacillus anthraciss  B Bacteria (expressed in E. coli), 3.10 Å
The structure is the PA 8LF 4 prechannel.
Feld et al. (2010).
Feld GK, Thoren KL, Kintzer AF, Sterling HJ, Tang II, Greenberg SG, Williams ER, & Krantz BA (2010). Structural basis for the unfolding of anthrax lethal factor by protective antigen oligomers.
Nat Struct Mol Biol 17 :1383-1390.
PubMed Id: 21037566.
Anthrax protective antigen pore: Bacillus anthracis  B Bacteria (expressed in E. coli), 2.9 Å
cryo-EM structure
Jiang et al. (2015).
Jiang J, Pentelute BL, Collier RJ, & Zhou ZH (2015). Atomic structure of anthrax protective antigen pore elucidates toxin translocation.
Nature 521 :545-549.
PubMed Id: 25778700.
doi: 10.1038/nature14247.
Lymphocyte preforin monomer: Mus musculus  E Eukaryota (expressed in S. frugiperda), 2.75 Å
The multimeric pore structure has been visualized by cryo-EM.
Law et al. (2010).
Law RH, Lukoyanova N, Voskoboinik I, Caradoc-Davies TT, Baran K, Dunstone MA, D'Angelo ME, Orlova EV, Coulibaly F, Verschoor S, Browne KA, Ciccone A, Kuiper MJ, Bird PI, Trapani JA, Saibil HR, & Whisstock JC (2010). The structural basis for membrane binding and pore formation by lymphocyte perforin.
Nature 468 :447-451.
PubMed Id: 21037563.
Cytolysin pore-forming toxin: Vibrio cholerae  B Bacteria (expressed in E. coli), 2.88 Å
Reveals the full structure of the assembled heptameric pore. The pore has a novel ring of tryptophan residues lining the narrowest constriction.
De & Olson (2011).
De S & Olson R. (2011). Crystal structure of the Vibrio cholerae cytolysin heptamer reveals common features among disparate pore-forming toxins
Proc Natl Acad Sci USA 108 :7385-7390.
PubMed Id: 21502531.
doi: 10.1073/pnas.1017442108.
Cytolysin pore-forming toxin protomer: Vibrio cholerae  B Bacteria (expressed in E. coli), 2.30 Å
Olson & Gouaux (2005).
Olson R & Gouaux E (2005). Crystal structure of the Vibrio cholerae cytolysin (VCC) pro-toxin and its assembly into a heptameric transmembrane pore
J Mol Biol 350 :997-1016.
PubMed Id: 15978620 .
doi: 10.1016/j.jmb.2005.05.045.
Streptolysin O pore-forming toxin: Streptococcus pyogenes  B Bacteria (expressed in E. coli), 2.10 Å
Feil et al. (2014).
Feil SC, Ascher DB, Kuiper MJ, Tweten RK, & Parker MW (2014). Structural Studies of Streptococcus pyogenes Streptolysin O Provide Insights into the Early Steps of Membrane Penetration.
J Mol Biol 426 :785-792.
PubMed Id: 24316049.
doi: 10.1016/j.jmb.2013.11.020.
Aerolysin pore-forming toxin Y221G mutant: Aeromonas hydrophila  B Bacteria (expressed in Aeromonas salmonicida), 2.88 Å
Y221G mutant, 2.20 Å: 3C0N
Y221G mutant in complex with mannose-6-phosphate, 2.50 Å: 3C0O
The paper shows models of the assembled heptameric pore.
Degiacomi et al. (2013).
Degiacomi MT, Iacovache I, Pernot L, Chami M, Kudryashev M, Stahlberg H, van der Goot FG, & Dal Peraro M (2013). Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism.
Nat Chem Biol 9 10:623-629.
PubMed Id: 23912165.
doi: 10.1038/nchembio.1312.
Monalysin pore-forming toxin, cleaved form: Pseudomonas entomophila  B Bacteria (expressed in E. coli), 1.70 Å
mutant deleted of the membrane-spanning domain, 2.65 Å: 4MKQ
EM structure deposited in EMBD as EMD-2698.
Leone et al. (2015).
Leone P, Bebeacua C, Opota O, Kellenberger C, Klaholz B, Orlov I, Cambillau C, Lemaitre B, & Roussel A (2015). X-ray and Cryo-electron Microscopy Structures of Monalysin Pore-forming Toxin Reveal Multimerization of the Pro-form.
J Biol Chem 290 :13191-13201.
PubMed Id: 25847242.
doi: 10.1074/jbc.M115.646109.
poly-C9 component of the complement membrane attack Complex: Homo sapiens  E Eukaryota, 8 Å
model from cryo-EM
Dudkina et al. (2016).
Dudkina NV, Spicer BA, Reboul CF, Conroy PJ, Lukoyanova N, Elmlund H, Law RH, Ekkel SM, Kondos SC, Goode RJ, Ramm G, Whisstock JC, Saibil HR, & Dunstone MA (2016). Structure of the poly-C9 component of the complement membrane attack complex.
Nat Commun 7 .
PubMed Id: 26841934.
doi: 10.1038/ncomms10588.


See also:
Serna et al. (2016).
Serna M, Giles JL, Morgan BP, & Bubeck D (2016). Structural basis of complement membrane attack complex formation.
Nat Commun 7 :10587.
PubMed Id: 26841837.
doi: 10.1038/ncomms10587.
Lysenin Pore complex: Eisenia fetida  B Bacteria (expressed in E. coli), 3.1 Å
cryo-EM structure
Bokori-Brown et al. (2016).
Bokori-Brown M, Martin TG, Naylor CE, Basak AK, Titball RW, & Savva CG (2016). Cryo-EM structure of lysenin pore elucidates membrane insertion by an aerolysin family protein.
Nat Commun 7 :11293.
PubMed Id: 27048994.
doi: 10.1038/ncomms11293.
ILYml Cholesterol-dependent cytolysin, CD59-responsive: Streptococcus intermedius  B Bacteria (expressed in E. coli), 2.89 Å
ILY ml = monomer-locked via a disulfide.
Bound to CD59 D22A, 2.7 Å: 5IMT
Lawrence et al. (2016).
Lawrence SL, Gorman MA, Feil SC, Mulhern TD, Kuiper MJ, Ratner AJ, Tweten RK, Morton CJ, & Parker MW (2016). Structural Basis for Receptor Recognition by the Human CD59-Responsive Cholesterol-Dependent Cytolysins.
Structure 24 :1488-1498.
PubMed Id: 27499440.
doi: 10.1016/j.str.2016.06.017.
VLYml Cholesterol-dependent cytolysin, CD-59 responsive, bound to CD59D22A: Gardnerella vaginalis  B Bacteria (expressed in E. coli), 2.4 Å
VLY ml = monomer locked via a disulfide
Lawrence et al. (2016).
Lawrence SL, Gorman MA, Feil SC, Mulhern TD, Kuiper MJ, Ratner AJ, Tweten RK, Morton CJ, & Parker MW (2016). Structural Basis for Receptor Recognition by the Human CD59-Responsive Cholesterol-Dependent Cytolysins.
Structure 24 :1488-1498.
PubMed Id: 27499440.
doi: 10.1016/j.str.2016.06.017.
Pneumolysin (PLY) complex: Streptococcus pneumoniae  B Bacteria (expressed in E. coli), 4.5 Å
cryo-EM structure
x-ray structure of PLY D168A monomer, 2.5 Å: 5AOE
x-ray structure of PLY Δ146/147 monomer, 2.45 Å: 5AOF
van Pee et al. (2017).
van Pee K, Neuhaus A, D'Imprima E, Mills DJ, Kühlbrandt W, & Yildiz Ö (2017). CryoEM structures of membrane pore and prepore complex reveal cytolytic mechanism of Pneumolysin.
Elife 6 :e23644.
PubMed Id: 28323617.
doi: 10.7554/eLife.23644.
Gasdermin (GSDM) Family
Gasdermins are multi-subunit β-barrel forming proteins
The gasdermins are expressed in the skin, mucosa, and immune antigen-presenting cells.
Gasdermin GSDMA3-NT pore: Mus musculus  E Eukaryota (expressed in E. coli), 3.8 Å
cryo-EM structure. C27-symmetry.
monomer crystal structure, 1.90 Å: 5B5R
Ruan et al. (2018).
Ruan J, Xia S, Liu X, Lieberman J, & Wu H (2018). Cryo-EM structure of the gasdermin A3 membrane pore.
Nature 557 7703:62-67.
PubMed Id: 29695864.
doi: 10.1038/s41586-018-0058-6.
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Adventitious Membrane Proteins: Alpha-helical Pore-forming Toxins.
Cytolysin A (ClyA, aka HlyE): Escherichia coli  B Bacteria, 3.29 Å
Mueller et al. (2009).
Mueller M, Grauschopf U, Maier T, Glockshuber R, & Ban N (2009). The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism.
Nature 459 :726-730.
PubMed Id: 19421192.
Cry6Aa toxin: Bacillus thuringiensis  B Bacteria (expressed in Pseudomonas fluorescens), 2.7 Å
trypsin-cleaved, 2.0 Å: 5KUC
supersedes 5J65.
Dementiev et al. (2016).
Dementiev A, Board J, Sitaram A, Hey T, Kelker MS, Xu X, Hu Y, Vidal-Quist C, Chikwana V, Griffin S, McCaskill D, Wang NX, Hung SC, Chan MK, Lee MM, Hughes J, Wegener A, Aroian RV, Narva KE, & Berry C (2016). The pesticidal Cry6Aa toxin from Bacillus thuringiensis is structurally similar to HlyE-family alpha pore-forming toxins.
BMC Biol 14 :71.
PubMed Id: 27576487.
doi: 10.1186/s12915-016-0295-9.
FraC eukaryotic pore-forming toxin from sea anemone: Actinia fragacea  E Eukaryota, 1.80 Å
Mechaly et al. (2011).
Mechaly AE, Bellomio A, Gil-Cartón D, Morante K, Valle M, González-Mañas JM, & Guérin DM (2011). Structural insights into the oligomerization and architecture of eukaryotic membrane pore-forming toxins.
Structure 19 :181-191.
PubMed Id: 21300287.
FraC toxin pore with bound lipids: Actinia fragacea  E Eukaryota (expressed in E. coli), 3.14 Å
Water soluble monomer (I), 1.70 Å: 3VWI
Water soluble monomer (II), 2.10 Å: 3W9P
Dimer with phosphorylcholine (I), 1.60 Å: 4TSL
Dimer with phosphorylcholine (II), 1.57 Å: 4TSN
Lipid (DHPC) bound (I), 2.30 Å: 4TSO
Lipid (DHPC) bound (II), 2.15 Å: 4TSP
Lipid (DHPC) bound (III), 1.60 Å: 4TSQ
Tanaka et al. (2015).
Tanaka K, Caaveiro JM, Morante K, González-Mañas JM, & Tsumoto K (2015). Structural basis for self-assembly of a cytolytic pore lined by protein and lipid.
Nat Commun 6 :6337.
PubMed Id: 25716479.
doi: 10.1038/ncomms7337.
Dermicidin hexameric anti-microbial peptide channel: Homo sapiens  E Eukaryota (expressed in Synthetic construct), 2.49 Å
Song et al. (2013).
Song C, Weichbrodt C, Salnikov ES, Dynowski M, Forsberg BO, Bechinger B, Steinem C, de Groot BL, Zachariae U, & Zeth K (2013). Crystal structure and functional mechanism of a human antimicrobial membrane channel.
Proc Natl Acad Sci USA 110 :4586-4591.
PubMed Id: 23426625.
doi: 10.1073/pnas.1214739110.
Tc Toxin, TcA prepore (TcdA1) subunit: Photorhabdus luminescens  B Bacteria (expressed in E. coli), 3.50 Å
TcB-TcC (TcdB2-TccC3) subunits, 2.17 Å: 4O9X
See also EM structures deposited in Electron Microscopy Data Bank under accession numbers EMD-2551 and EMD-2552.
Meusch et al. (2014).
Meusch D, Gatsogiannis C, Efremov RG, Lang AE, Hofnagel O, Vetter IR, Aktories K, & Raunser S (2014). Mechanism of Tc toxin action revealed in molecular detail.
Nature 508 :61-65.
PubMed Id: 24572368.
doi: 10.1038/nature13015.
Tc Toxin, TcA pore (TcdA1) embedded in lipid nanodiscs using flexible fitting: Photorhabdus luminescens  B Bacteria (expressed in E. coli), 3.46 Å
cryo-EM structure.
without flexible fitting, 3.46 Å: 5LKI
Gatsogiannis et al. (2016).
Gatsogiannis C, Merino F, Prumbaum D, Roderer D, Leidreiter F, Meusch D, & Raunser S (2016). Membrane insertion of a Tc toxin in near-atomic detail.
Nat Struct Mol Biol 23 :884-890.
PubMed Id: 27571177.
doi: 10.1038/nsmb.3281.
Listeriolysin O pore-forming toxin: Listeria monocytogenes  B Bacteria, 2.15 Å
A model of the assembled pore contains 36 monomers. In that configuration, the membrane-spanning region of the toxin is a mix of α-helices and β-sheets
Köster et al. (2014).
Köster S, van Pee K, Hudel M, Leustik M, Rhinow D, Kühlbrandt W, Chakraborty T, & Yildiz O (2014). Crystal structure of listeriolysin O reveals molecular details of oligomerization and pore formation.
Nat Commun 5 :3690.
PubMed Id: 24751541.
doi: 10.1038/ncomms4690.
XaxAB pore complex: Xenorhabdus nematophila  B Bacteria (expressed in E. coli), 4 Å
cryo-EM structure
x-ray structure of XaxA monomer, 2.5 Å: 6GY8
x-ray structure of XaxB monomer, 3.4 Å: 6GY7
Schubert et al. (2018).
Schubert E, Vetter IR, Prumbaum D, Penczek PA, & Raunser S (2018). Membrane insertion of α-xenorhabdolysin in near-atomic detail.
Elife 7 :e38017.
PubMed Id: 30010541.
doi: 10.7554/eLife.38017.
De novo Designed Membrane Proteins
Functional Proteins Designed from First Principles
Zn2+-transporting four-helix bundle (space group P43212): De novo designed  U Unclassified, 2.80 Å
Space group I4 122, 2.70 Å: 4P6K
Space group I2 13, 2.80 Å: 4P6L
NMR structure: 2MUZ
Joh et al. (2014).
Joh NH, Wang T, Bhate MP, Acharya R, Wu Y, Grabe M, Hong M, Grigoryan G, & DeGrado WF (2014). De novo design of a transmembrane Zn 2+-transporting four-helix bundle.
Science 346 6216:1520-1524.
PubMed Id: 25525248.
doi: 10.1126/science.1261172.
Transmembrane protein TMHC2_E: De novo designed protein  U Unclassified (expressed in E. coli), 2.95 Å
Transmembrane protein TMHC4_R, 3.89 Å: 6B85
Lu et al. (2018).
Lu P, Min D, DiMaio F, Wei KY, Vahey MD, Boyken SE, Chen Z, Fallas JA, Ueda G, Sheffler W, Mulligan VK, Xu W, Bowie JU, & Baker D (2018). Accurate computational design of multipass transmembrane proteins.
Science 359 6379:1042-1046.
PubMed Id: 29496880.
doi: 10.1126/science.aaq1739.
Outer Membrane Proteins
Wza translocon for capsular polysaccharides: Escherichia coli  B Bacteria, 2.25 Å
The first outer membrane protein that penetrates the membrane as an alpha-helix bundle. The intact protein is comprised of eight monomers.
Dong et al. (2006).
Dong C, Beis K, Nesper J, Brunkan-LaMontagne AL, Clarke BR JM, Whitfield C, & Naismith JH (2006). Wza the translocon for E. coli. capsular polysaccharides defines a new class of membrane protein.
Nature 444 :226-229.
PubMed Id: 17086202.
Porin B monomer: Corynebacterium glutamicum  B Bacteria (expressed in Escherichia coli), 1.82 Å
Putative helical porin, probably comprised of five monomers. Crystal form I.
Crystal form II, 2.89 Å: 2VQH
Crystal form IV, 4.20 Å: 2VQK
Crystal form III, 3.16 Å: 2VQL
Ziegler et al. (2008).
Ziegler K, Benz R, & Schulz GE (2008). A putative alpha-helical porin from Corynebacterium glutamicum.
J Mol Biol 379 :482-491.
PubMed Id: 18462756.
Type IV outer membrane secretion complex: Escherichia coli  B Bacteria, 2.60 Å
Comprised of 14 copies each of TraF, TraO, and TraN; 590 kDa.
Chandran et al. (2009).
Chandran V, Fronzes R, Duquerroy S, Cronin N, Navaza J, & Waksman G (2009). Structure of the outer membrane complex of a type IV secretion system.
Nature 462 :1011-1015.
PubMed Id: 19946264.
MlaA lipid transport protein in complex with OmpF: Klebsiella pneumoniae  B Bacteria (expressed in E. coli), 3.2 Å
in complex with OmpK36, 2.9 Å: 5NUP
Serratia marcescens MlaA in complex with OmpF, 3.2 Å: 5NUQ
in complex with OmpF and LPS, 3.29 Å: 5NUR
Abellón-Ruiz et al. (2017).
Abellón-Ruiz J, Kaptan SS, Baslé A, Claudi B, Bumann D, Kleinekathöfer U, & van den Berg B (2017). Structural basis for maintenance of bacterial outer membrane lipid asymmetry.
Nat Microbiol 2 12:1616-1623.
PubMed Id: 29038444.
doi: 10.1038/s41564-017-0046-x.
Bacterial Cell Divison Proteins
These proteins comprise the so-called 'divisome'
CrgA cell division structural & regulatory protein: Mycobacterium tuberculosis  B Bacteria (expressed in E. coli), NMR Structure
Structure of protein determined using both oriented sample and magic-angle spinning NMR data from liquid-crystalline lipid bilayer preparation.
Das et al. (2015).
Das N, Dai J, Hung I, Rajagopalan MR, Zhou HX, & Cross TA (2015). Structure of CrgA, a cell division structural and regulatory protein from Mycobacterium tuberculosis, in lipid bilayers.
Proc Natl Acad Sci USA 112 2:E119-E126.
PubMed Id: 25548160.
doi: 10.1073/pnas.1415908112.
Bacterial and Algal Rhodopsins
Bacteriorhodopsin (BR): Halobacterium salinarum  A Archaea, 3.5 Å
Electron Diffraction. The first atomic-resolution structure of bacteriorhodopsin
Grigorieff et al. (1996).
Grigorieff N, Ceska TA, Downing KH, Baldwin JM, & Henderson R (1996). Electron-crystallographic refinement of the structure of bacteriorhodopsin.
J Mol Biol 259 :393-421.
PubMed Id: 8676377.
Bacteriorhodopsin (BR): Halobacterium salinarum  A Archaea, 3.0 Å
Electron Diffraction
Kimura et al. (1997).
Kimura Y, Vassylyev DG, Miyazawa A, Kidera A, Matsushima M, Mitsuok a K, Murata K, Hirai T, & Fujiyoshi Y (1997). Surface of bacteriorhodopsin revealed by high-resolution electron crystallography.
Nature 389 :206-211.
PubMed Id: 8676377.
Bacteriorhodopsin (BR): Halobacterium salinarum  A Archaea, 2.35 Å
The first x-ray structure of bacteriorhodopsin
Pebay-Peyroula et al. (1997).
Pebay-Peyroula E, Rummel G, Rosenbusch JP, & Landau EM (1997). X-ray structure of bacteriorhodopsin at 2.5 Å from microcrystals grown in lipidic cubic phases.
Science 277 :1676-1681.
PubMed Id: 9287223.
Bacteriorhodopsin (BR): Halobacterium salinarum  A Archaea, 2.90 Å
Essen et al. (1998).
Essen L, Siegert R, Lehmann WD, & Oesterhelt D (1998). Lipid patches in membrane protein oligomers: crystal structure of the bacteriorhodopsin-lipid complex.
Proc Natl Acad Sci U S A 95 :11673-11678.
PubMed Id: 9751724.
Bacteriorhodopsin (BR): Halobacterium salinarum  A Archaea, 2.30 Å
Luecke et al. (1998).
Luecke H, Richter HT, & Lanyi JK (1998). Proton transfer pathways in bacteriorhodopsin at 2.3 Angstrom resolution.
Science 280 :1934-1937.
PubMed Id: 9632391.
Bacteriorhodopsin (BR) dark-adapted: Halobacterium salinarum  A Archaea, NMR structure
Patzelt et al. (2002).
Patzelt H, Simon B, terLaak A, Kessler B, Kühne R, Schmieder P, Oesterhelt D, & Oschkinat H (2002). The structures of the active center in dark-adapted bacteriorhodopsin by solution-state NMR spectroscopy.
Proc Natl Acad Sci USA 99 :9765-9770.
PubMed Id: 12119389.
Bacteriorhodopsin (BR), K intermediate: Halobacterium salinarum  A Archaea, 2.10 Å
R-free = O.255. R-free = 0.303, 2.1 Å: 1QKO
Edman et al. (1999).
Edman K, Nollert P, Royant A, Belrhali H, Pebay-Peyroula E, Hajdu J, Neutze R, & Landau EM (1999). High-resolution X-ray structure of an early intermediate in the bacteriorhodopsin photocycle.
Nature 401 :822-826.
PubMed Id: 10548112.
Bacteriorhodopsin (BR), K intermediate (illuminated): Halobacterium salinarum  A Archaea, 1.43 Å
Non-illuminated, 1.47 Å: 1M0L
Schobert et al. (2002).
Schobert B, Cupp-Vickery J, Hornak V, Smith S, & Lanyi J (2002). Crystallographic structure of the K intermediate of bacteriorhodopsin: conservation of free energy after photoisomerization of the retinal.
J. Mol. Biol. 321 :715-726.
PubMed Id: 12206785.
Bacteriorhodopsin in an early-M intermediate state: Halobacterium salinarum  A Archaea, 2.00 Å
In "mock-trapped" early-M intermediate state, 1.81 Å: 1KG9
In ground state, 1.65 Å: 1KGB
Facciotti et al. (2001).
Facciotti MT, Rouhani S, Burkard FT, Betancourt FM, Downing KH, Rose RB, McDermott G, & Glaeser RM (2001). Structure of an early intermediate in the M-state phase of the bacteriorhodopsin photocycle
Biophys J 81 :3442-3455.
PubMed Id: 11721006.
doi: 10.1016/S0006-3495(01)75976-0.
Bacteriorhodopsin (BR): Halobacterium salinarum  A Archaea, 1.90 Å
Belrhali et al. (1999).
Belrhali H, Nollert P, Royant A, Menzel C, Rosenbusch JP, Landau EH, & Pebay-Peyroula E (1999). Protein, lipid, and water organization in bacteriorhodopsin crystals: A molecular view of the purple membrane at 1.9 Å resolution.
Structure 7 :909-917.
PubMed Id: 10467143.
Bacteriorhodopsin (BR): Halobacterium salinarum  A Archaea, 1.55 Å
Luecke et al. (1999).
Luecke H, Schobert B, Richter HT, Cartailler P, & Lanyi JK (1999). Structure of bacteriorhodopsin at 1.55 angstrom resolution.
J. Mol. Biol 291 :899-911.
PubMed Id: 10452895.
Bacteriorhodopsin (BR), D96N in bR state: Halobacterium salinarum  A Archaea, 1.80 Å
D96N in M-state, 2.00 Å: 1C8S.
Luecke et al. (1999).
Luecke H, Schobert B, Richter HT, Cartailler P, & Lanyi JK (1999). Structural changes in bacteriorhodopsin during ion transport at 2 angstrom resolution.
Science 286 :255-260.
PubMed Id: 10514362.
Bacteriorhodopsin in ground state: Halobacterium salinarum  A Archaea, 1.78 Å
Ground state, after x-ray modification, 1.78 Å: 3NSB
Borshchevskiy et al. (2011).
Borshchevskiy VI, Round ES, Popov AN, Büldt G, & Gordeliy VI (2011). X-ray-Radiation-Induced Changes in Bacteriorhodopsin Structure
J Mol Biol 409 :813-825.
PubMed Id: 21530535.
doi: 10.1016/j.jmb.2011.04.038.
Bacteriorhodopsin phototaxis signalling mutant (A215T): Halobacterium sp. nrc-1  A Archaea (expressed in Halobacterium salinarum), 3.01 Å
This mutant enables BR's photochemical reactions to transmit signals to the transducer HtrII.
Spudich et al. (2012).
Spudich EN, Ozorowski G, Schow EV, Tobias DJ, Spudich JL, & Luecke H (2012). A transporter converted into a sensor, a phototaxis signaling mutant of bacteriorhodopsin at 3.0 Å.
J Mol Biol 415 :455-463.
PubMed Id: 22123198.
doi: 10.1016/j.jmb.2011.11.025.
Bacteriorhodopsin (BR); D96/F171C/F219L mutant: Halobacterium salinarum  A Archaea, 2.65 Å
Wang et al. (2013).
Wang T, Sessions AO, Lunde CS, Rouhani S, Glaeser RM, Duan Y, & Facciotti MT (2013). Deprotonation of D96 in bacteriorhodopsin opens the proton uptake pathway.
Structure 21 :290-297.
PubMed Id: 23394942.
doi: 10.1016/j.str.2012.12.018.
Bacteriorhodopsin (BR) determined using serial ms crystallography (SMX): Halobacterium salinarum  A Archaea, 2.40 Å
Structure by conventional crystallography, 1.90 Å: 4X32
Nogly et al. (2015).
Nogly P, James D, Wang D, White TA, Zatsepin N, Shilova A, Nelson G, Liu H, Johansson L, Heymann M, Jaeger K, Metz M, Wickstrand C, Wu W, Båth P, Berntsen P, Oberthuer D, Panneels V, Cherezov V, Chapman H, Schertler G, Neutze R, Spence J, Moraes I, Burghammer M, Standfuss J, & Weierstall U (2015). Lipidic cubic phase serial millisecond crystallography using synchrotron radiation.
IUCrJ 2 :168-176.
PubMed Id: 25866654.
doi: 10.1107/S2052252514026487.
Bacteriorhodopsin (BR) native: Halobacterium salinarum  A Archaea, 2.35 Å
Structure determind by XFEL. Crystallized from bicelles.
Crystallized from Bicelles in Complex with Iodine-labeled Detergent HAD13a, 2.1 Å: 5B34
Nakane et al. (2016).
Nakane T, Hanashima S, Suzuki M, Saiki H, Hayashi T, Kakinouchi K, Sugiyama S, Kawatake S, Matsuoka S, Matsumori N, Nango E, Kobayashi J, Shimamura T, Kimura K, Mori C, Kunishima N, Sugahara M, Takakyu Y, Inoue S, Masuda T, Hosaka T, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Inoue T, Nureki O, Iwata S, Murata M, & Mizohata E (2016). Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent.
Proc Natl Acad Sc. USA 113 :13039-13044.
PubMed Id: 27799539.
Bacteriorhodopsin (BR) 3D movie, ground state: Halobacterium salinarum  A Archaea, 2.0 Å
See the movie: http://science.sciencemag.org/content/sci/suppl/2016/12/21/354.6319.1552.DC1/aah3497s1.mp4

structure at:
16 nsec, 2.1 Å: 5B6W
40 nsec, 2.1 Å: 5H2H
110 nsec, 2.1 Å: 5H2I
290 nsec, 2.1 Å: 5H2J
760 nsec, 2.1 Å: 5B6X
2 μsec, 2.1 Å: 5H2K
5.25 μsec, 2.1 Å: 5H2L
13.8 μsec, 2.1 Å: 5H2M
36.2 μsec, 2.1 Å: 5B6Y
95.2 μsec, 2.1 Å: 5H2N
250 μsec, 2.1 Å: 5H2O
657 μsec, 2.1 Å: 5H2P
1.725 msec, 2.1 Å: 5B6Z
Nango et al. (2016).
Nango E, Royant A, Kubo M, Nakane T, Wickstrand C, Kimura T, Tanaka T, Tono K, Song C, Tanaka R, Arima T, Yamashita A, Kobayashi J, Hosaka T, Mizohata E, Nogly P, Sugahara M, Nam D, Nomura T, Shimamura T, Im D, Fujiwara T, Yamanaka Y, Jeon B, Nishizawa T, Oda K, Fukuda M, Andersson R, Båth P, Dods R, Davidsson J, Matsuoka S, Kawatake S, Murata M, Nureki O, Owada S, Kameshima T, Hatsui T, Joti Y, Schertler G, Yabashi M, Bondar AN, Standfuss J, Neutze R, & Iwata S (2016). A three-dimensional movie of structural changes in bacteriorhodopsin.
Science 354 :1552-1557.
PubMed Id: 28008064.
doi: 10.1126/science.aah3497.
Bacteriorhodopsin (BR) retinal isomerization movie, ground state: Halobacterium salinarum  A Archaea, 1.5 Å
see the movie: http://science.sciencemag.org/highwire/filestream/711278/field_highwire_adjunct_files/3/aat0094s3.mov
Δt 49 - 406 fs, 1.9 Å: 6G7I
Δt 457-646 fs, 1.9 Å: 6G7J
Δt 10 ps, 1.9 Å: 1.9 Å: 6G7K
Δt 8.3 ms, 1.9 Å: 6G7L
Nogly et al. (2018).
Nogly P, Weinert T, James D, Carbajo S, Ozerov D, Furrer A, Gashi D, Borin V, Skopintsev P, Jaeger K, Nass K, Båth P, Bosman R, Koglin J, Seaberg M, Lane T, Kekilli D, Brünle S, Tanaka T, Wu W, Milne C, White T, Barty A, Weierstall U, Panneels V, Nango E, Iwata S, Hunter M, Schapiro I, Schertler G, Neutze R, & Standfuss J (2018). Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser.
Science .
PubMed Id: 29903883.
doi: 10.1126/science.aat0094.
Bacteriorhodopsin (BR), trimer in asymmetric unit: Haloquadratum walsbyi  A Archaea (expressed in E. coli), 1.85 Å
This BR pumps protons efficiently under acid conditions.
antiparallel dimer in asymmetric unit, 2.57 Å: 4QID
Hsu et al. (2015).
Hsu MF, Fu HY, Cai CJ, Yi HP, Yang CS, & Wang AH (2015). Structural and Functional Studies of a Newly Grouped Haloquadratum walsbyi Bacteriorhodopsin Reveal the Acid-resistant Light-driven Proton Pumping Activity.
J Biol Chem 290 :29567-29577.
PubMed Id: 26483542.
doi: 10.1074/jbc.M115.685065.
Bacteriorhodopsin (BR) crystallized from octylglucoside (OG) detergent micelles: Haloquadratum walsbyi  A Archaea (expressed in E. coli), 2.18 Å
crystallized from styrene maleic acid (SMA) polymer nanodiscs, 2.0 Å: 5ITC
Broecker et al. (2017).
Broecker J, Eger BT, & Ernst OP (2017). Crystallogenesis of Membrane Proteins Mediated by Polymer-Bounded Lipid Nanodiscs.
Structure 25 :384-392.
PubMed Id: 28089451.
doi: 10.1016/j.str.2016.12.004.
Halorhodopsin (HR): Halobacterium salinarum  A Archaea, 1.8 Å
Kolbe et al. (2000).
Kolbe M, Besir H, Essen L-O, & Oesterhelt D (2000). Structure of the light-driven chloride pump halorhodopsin at 1.8 Å.
Science 288 :1390-1396.
PubMed Id: 10827943.
Halorhodopsin (HR): Natronomonas pharaonis  A Archaea, 2.0 Å
Kouyama et al. (2010).
Kouyama T, Kanada S, Takeguchi Y, Narusawa A, Murakami M, Ihara K. (2010). Crystal Structure of the Light-Driven Chloride Pump Halorhodopsin from Natronomonas pharaonis.
J Mol Biol 396 :564-579.
PubMed Id: 19961859.
Sensory Rhodopsin: Anabaena (Nostoc) sp. PCC7120  B Bacteria, 2.0 Å
Vogeley et al. (2004).
Vogeley L, Sineshchekov OA, Trivedi VD, Sasaki J, Spudich JL, & Luecke H (2004). Anabaena sensory rhodopsin: a photochromic color sensor at 2.0 Å.
Science 306 :1390-1393.
PubMed Id: 15459346.
Sensory Rhodopsin: Anabaena (Nostoc) sp. PCC7120  B Bacteria (expressed in E. coli), NMR Structure
Wang et al. (2013).
Wang S, Munro RA, Shi L, Kawamura I, Okitsu T, Wada A, Kim SY, Jung KH, Brown LS, & Ladizhansky V (2013). Solid-state NMR spectroscopy structure determination of a lipid-embedded heptahelical membrane protein.
Nat Methods 10 :1007-1012.
PubMed Id: 24013819.
doi: 10.1038/nmeth.2635.
Sensory Rhodopsin II (SRII): Natronomonas pharaonis  A Archaea, 2.40 Å
Luecke et al. (2001).
Luecke H, Schobert B, Lanyi JK, Spudich EN, & Spudich JL (2001). Crystal structure of sensory rhodopsin II at 2.4 Å: Insights into color tuning and transducer interaction.
Science 293 :1499-1503.
PubMed Id: 11452084.
Sensory Rhodopsin II (SRII): Natronomonas pharaonis  A Archaea (expressed in E. coli), 2.10 Å
Royant et al. (2001).
Royant A, Nollert P, Edman K, Neutze R, Landau EM, & Pebay-Peyroula E. (2001). X-ray structure of sensory rhodopsin II at 2.1 Å resolution.
Proc Natl Acad Sci USA 98 :10131-10136.
PubMed Id: 11504917.
Sensory Rhodopsin II (SRII) with transducer: Natronomonas pharaonis  A Archaea (expressed in E. coli), 1.93 Å
Gordeliy et al. (2002).
Gordeliy VI, Labahn J, Moukhametzianov R, Efremov R, Granzin J, Schlesinger R, Büldt G, Savopol T, Scheidig AJ, Klare JP, & Engelhard M. (2002). Molecular basis of transmembrane signalling by sensory rhodopsin II-transducer complex.
Nature 419 :484-487.
PubMed Id: 12368857.
Sensory Rhodopsin II (SRII): Natronomonas pharaonis  A Archaea (expressed in E. coli), NMR structure
Gautier et al. (2010).
Gautier A, Mott HR, Bostock MJ, Kirkpatrick JP, & Nietlispach D (2010). Structure determination of the seven-helix transmembrane receptor sensory rhodopsin II by solution NMR spectroscopy.
Nat Struct Mol Biol 17 :768-774.
PubMed Id: 20512150.
Sensory Rhodopsin II (SRII) in active state: Natronomonas pharaonis  A Archaea (expressed in E. coli), 2.50 Å
SR II in ground state, 1.90 Å: 3QAP
Gushchin et al. (2011).
Gushchin I, Reshetnyak A, Borshchevskiy V, Ishchenko A, Round E, Grudinin S, Engelhard M, Büldt G, & Gordeliy V (2011). Active state of sensory rhodopsin II: structural determinants for signal transfer and proton pumping.
J Mol Biol 412 :591-600.
PubMed Id: 21840321.
doi: 10.1016/j.jmb.2011.07.022.
Archaerhodopsin-1 (aR-1): Halorubrum sp. aus-1  A Archaea, 3.4 Å
Enami et al. (2006).
Enami N, Yoshimura K, Murakami M, Okumura H, Ihara K, & Kouyama T. (2006). Crystal Structures of Archaerhodopsin-1 and -2: Common Structural Motif in Archaeal Light-driven Proton Pumps.
J Mol Biol 356 :675-685.
PubMed Id: 16540121.
Archaerhodopsin-2 (aR-2): Haloroubrum sp. aus-2  A Archaea, 2.5 Å
Enami et al. (2006).
Enami N, Yoshimura K, Murakami M, Okumura H, Ihara K, & Kouyama T. (2006). Crystal Structures of Archaerhodopsin-1 and -2: Common Structural Motif in Archaeal Light-driven Proton Pumps.
J Mol Biol 356 :675-685.
PubMed Id: 16540121.
Archaerhodopsin-2 (aR-2): Haloroubrum sp. aus-2  A Archaea, 2.10 Å
Crystallized with the carotenoid bacterioruberin, space group P321.
Space group P6 3, 2.50 Å: 2Z55.
Yoshimura & Kouyama. (2008).
Yoshimura K & Kouyama T (2008). Structural role of bacterioruberin in the trimeric structure of archaerhodopsin-2.
J Mol Biol 375 :1267-1281.
PubMed Id: 18082767.
Archaerhodopsin-2 (aR-2): Haloroubrum sp. aus-2  A Archaea, 1.80 Å
Kouyama et al. (2014).
Kouyama T, Fujii R, Kanada S, Nakanishi T, Chan SK, & Murakami M (2014). Structure of archaerhodopsin-2 at 1.8?Å resolution.
Acta Crystallogr D Biol Crystallogr 70 :2692-2701.
PubMed Id: 25286853.
doi: 10.1107/S1399004714017313.
Xanthorhodopsin: Salinibacter ruber  B Bacteria, 1.9 Å
Contains bound carotenoid.
Luecke et al. (2008).
Luecke H, Schobert B, Stagno J, Imasheva ES, Wang JM, Balashov SP, & Lanyi JK (2008). Crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore.
Proc Natl Acad Sci USA 105 :16561-16565.
PubMed Id: 18922772.
Acetabularia Rhodopsin II (ARII): Acetabularia acetabulum  E Eukaryota (expressed in cell-free expression), 3.20 Å
This the first structure of a eukaryotic light-driven proton pump
Wada et al. (2011).
Wada T, Shimono K, Kikukawa T, Hato M, Shinya N, Kim SY, Kimura-Someya T, Shirouzu M, Tamogami J, Miyauchi S, Jung KH, Kamo N, & Yokoyama S (2011). Crystal Structure of the Eukaryotic Light-Driven Proton-Pumping Rhodopsin, Acetabularia Rhodopsin II, from Marine Alga
J Mol Biol 411 :986-998.
PubMed Id: 21726566.
doi: 10.1016/j.jmb.2011.06.028.
Channelrhodopsin (ChR) chimera between ChR1 & ChR2: Chlamydomonas reinhardtii  E Eukaryota (expressed in S. frugiperda), 2.30 Å
First ChR structure. Reveals cation conduction pathway.
Kato et al. (2012).
Kato HE, Zhang F, Yizhar O, Ramakrishnan C, Nishizawa T, Hirata K, Ito J, Aita Y, Tsukazaki T, Hayashi S, Hegemann P, Maturana AD, Ishitani R, Deisseroth K, & Nureki O (2012). Crystal structure of the channelrhodopsin light-gated cation channel.
Nature 482 :369-374.
PubMed Id: 22266941.
doi: 10.1038/nature10870.
Channelrhodopsin (ChR) chimera between ChR1 & ChR2, T198G/G202A mutant: Chlamydomonas reinhardtii  E Eukaryota (expressed in S. frugiperda), 2.50 Å
Blue-shifted mutant
Kato et al. (2015).
Kato HE, Kamiya M, Sugo S, Ito J, Taniguchi R, Orito A, Hirata K, Inutsuka A, Yamanaka A, Maturana AD, Ishitani R, Sudo Y, Hayashi S, & Nureki O (2015). Atomistic design of microbial opsin-based blue-shifted optogenetics tools.
Nat Commun 6 :7177.
PubMed Id: 25975962.
doi: 10.1038/ncomms8177.
Channelrhodopsin 2 (ChR2): Chlamydomonas reinhardtii  E Eukaryota (expressed in Leishmania tarentolae), 2.39 Å
C128T mutant, 2.7 Å: 6EIG
Volkov et al. (2017).
Volkov O, Kovalev K, Polovinkin V, Borshchevskiy V, Bamann C, Astashkin R, Marin E, Popov A, Balandin T, Willbold D, Büldt G, Bamberg E, Gordeliy V (2017). Structural insights into ion conduction by channelrhodopsin 2
Science 358 6366:eaan8862.
PubMed Id: 29170206.
doi: 10.1126/science.aan8862.
Proteorhodopsin (green-light absorbing) : Uncultured marine gamma proteobacterium ebac31a08  B Bacteria (expressed in E. coli-based cell-free expression system), NMR Structure
Reckel et al. (2011).
Reckel S, Gottstein D, Stehle J, Löhr F, Verhoefen MK, Takeda M, Silvers R, Kainosho M, Glaubitz C, Wachtveitl J, Bernhard F, Schwalbe H, Güntert P, Dötsch V (2011). Solution NMR structure of proteorhodopsin.
Angew Chem Int Ed Engl 50 :11942-11946.
PubMed Id: 22034093.
doi: 10.1002/anie.201105648.
Proteorhodopsin: Exiguobacterium sibiricum  B Bacteria (expressed in E. coli), 2.30 Å
Lysine is the proton donor in this novel proteorhodopsin
Gushchin et al. (2013).
Gushchin I, Chervakov P, Kuzmichev P, Popov AN, Round E, Borshchevskiy V, Ishchenko A, Petrovskaya L, Chupin V, Dolgikh DA, Arseniev AA, Kirpichnikov M, & Gordeliy V (2013). Structural insights into the proton pumping by unusual proteorhodopsin from nonmarine bacteria.
Proc Natl Acad Sci USA 110 :12631-12636.
PubMed Id: 23872846.
doi: 10.1073/pnas.1221629110.
Proteorhodopsin (blue-light absorbing), Med12BPR: uncultured bacterium  B Bacteria (expressed in E. coli), 2.31 Å
Isolated from the Mediterranean Sea at a depth of 12 m. Oligomerizes as a hexameric ring.
Ran et al. (2013).
Ran T, Ozorowski G, Gao Y, Sineshchekov OA, Wang W, Spudich JL, & Luecke H (2013). Cross-protomer interaction with the photoactive site in oligomeric proteorhodopsin complexes.
Acta Crystallogr D Biol Crystallogr 69 :1965-1980.
PubMed Id: 24100316.
Proteorhodopsin (blue-light absorbing); HOT75BPR, D97N mutant: gamma proteobacterium  B Bacteria (expressed in E. coli), 2.70 Å
Isolated from the Pacific Ocean near Hawaii at a depth of 75 m. Oligomerizes as a pentameric ring.
D97N/Q105L mutant, 2.60 Å: 4KNF
Ran et al. (2013).
Ran T, Ozorowski G, Gao Y, Sineshchekov OA, Wang W, Spudich JL, & Luecke H (2013). Cross-protomer interaction with the photoactive site in oligomeric proteorhodopsin complexes.
Acta Crystallogr D Biol Crystallogr 69 :1965-1980.
PubMed Id: 24100316.
Cruxrhodopsin-3 (cR3), pH 5: Haloarcula vallismortis  A Archaea (expressed in H. salinarum ), 2.10 Å
at pH 6, 2.30 Å: 4JR8
Chan et al. (2014).
Chan SK, Kitajima-Ihara T, Fujii R, Gotoh T, Murakami M, Ihara K, & Kouyama T (2014). Crystal Structure of Cruxrhodopsin-3 from Haloarcula vallismortis.
PLoS ONE 9 9:e108362.
PubMed Id: 25268964.
doi: 10.1371/journal.pone.0108362.
KR2 light-driven Na+ pump, acidic conditions: Dokdonia eikasta  B Bacteria (expressed in E. coli), 2.30 Å
basic conditions, 2.30 Å: 3X3C
Kato et al. (2015).
Kato HE, Inoue K, Abe-Yoshizumi R, Kato Y, Ono H, Konno M, Hososhima S, Ishizuka T, Hoque MR, Kunitomo H, Ito J, Yoshizawa S, Yamashita K, Takemoto M, Nishizawa T, Taniguchi R, Kogure K, Maturana AD, Iino Y, Yawo H, Ishitani R, Kandori H, & Nureki O (2015). Structural basis for Na + transport mechanism by a light-driven Na + pump.
Nature 521 :48-53.
PubMed Id: 25849775.
doi: 10.1038/nature14322.
KR2 light-driven Na+ pump, monomeric blue form at pH 4.3: Dokdonia eikasta  B Bacteria (expressed in E. coli), 1.45 Å
Pentameric red form at pH 4.9, 2.20 Å: 4XTN
Pentameric red form at pH 5.6, 1.45 Å: 4XTL
Gushchin et al. (2015).
Gushchin I, Shevchenko V, Polovinkin V, Kovalev K, Alekseev A, Round E, Borshchevskiy V, Balandin T, Popov A, Gensch T, Fahlke C, Bamann C, Willbold D, Büldt G, Bamberg E, & Gordeliy V (2015). Crystal structure of a light-driven sodium pump.
Nat Struct Mol Biol 22 :390-395.
PubMed Id: 25849142.
doi: 10.1038/nsmb.3002.
Thermophilic rhodopsin: Thermus thermophilus  B Bacteria (expressed in E. coli), 2.8 Å
Tsukamoto et al. (2016).
Tsukamoto T, Mizutani K, Hasegawa T, Takahashi M, Honda N, Hashimoto N, Shimono K, Yamashita K, Yamamoto M, Miyauchi S, Takagi S, Hayashi S, Murata T, & Sudo Y (2016). X-ray Crystallographic Structure of Thermophilic Rhodopsin.
J Biol Chem 291 23:12223-12232.
PubMed Id: 27129243.
doi: 10.1074/jbc.M116.719815.
NTQ chloride transport rhodopsin, type A crystal: Nonlabens marinus S1-08T  B Bacteria (expressed in E. coli), 1.57 Å
type B crystal, 2.0 Å: 5G54
Br ion crystal, 2.17 Å: 5G2A
T102N mutant, 1.80 Å: 5G2D
T102D mutant, 2.31 Å: 5G2C
Kim et al. (2016).
Kim K, Kwon SK, Jun SH, Cha JS, Kim H, Lee W, Kim JF, & Cho HS (2016). Crystal structure and functional characterization of a light-driven chloride pump having an NTQ motif.
Nat Commun 7 :12677.
PubMed Id: 27554809.
doi: 10.1038/ncomms12677.
Novel Receptors
Human sigma-1 (σ1) receptor, with bound PD144418: Homo sapiens  E Eukaryota (expressed in S. frugiperda), 2.51 Å
with bound 4-IBP, 3.2 Å: 5HK2
Schmidt et al. (2016).
Schmidt HR, Zheng S, Gurpinar E, Koehl A, Manglik A, & Kruse AC (2016). Crystal structure of the human σ 1 receptor.
Nature 532 :527-530.
PubMed Id: 27042935.
doi: 10.1038/nature17391.
STRA6 retinol-uptake receptor in complex with calmodulin (CaM): Danio rerio  E Eukaryota (expressed in sf9 cells), 3.9 Å
cryo-EM structure
Chen et al. (2016).
Chen Y, Clarke OB, Kim J, Stowe S, Kim YK, Assur Z, Cavalier M, Godoy-Ruiz R, von Alpen DC, Manzini C, Blaner WS, Frank J, Quadro L, Weber DJ, Shapiro L, Hendrickson WA, & Mancia F (2016). Structure of the STRA6 receptor for retinol uptake.
Science 353 .
PubMed Id: 27563101.
doi: 10.1126/science.aad8266.
Tetraspanins
Mediate essential functions in the immune, reproductive, genitourinary, and auditory systems
CD81 full-length tetraspanin: Homo sapiens  E Eukaryota (expressed in S. frugiperda), 2.95 Å
Zimmerman et al. (2016).
Zimmerman B, Kelly B, McMillan BJ, Seegar TC, Dror RO, Kruse AC, & Blacklow SC (2016). Crystal Structure of a Full-Length Human Tetraspanin Reveals a Cholesterol-Binding Pocket.
Cell 167 4:1041-1051.
PubMed Id: 27881302.
doi: 10.1016/j.cell.2016.09.056.
Autonomously Folding "Membrane Proteins" (Sec-independent)
Mistic membrane-integrating protein: Bacillus subtilis  B Bacteria, NMR structure
Note: This is not a membrane protein. It is included here because of general interest.
Roosild et al. (2005).
Roosild TP, Greenwald J, Vega M, Castronovo S, Riek R, & Choe S (2005). NMR structure of Mistic, a membrane-integrating protein for membrane protein expression.
Science 307 :1317-1321.
PubMed Id: 15731457.
Virus Coat Proteins
M13 Major Coat Protein in Dodecylphosphocholine micelles: Enterobacteria phage m13  V Viruses (expressed in E. coli), NMR Structure
In SDS micelles: 2CPS
Papavoine et al. (1998).
Papavoine CH, Christiaans BE, Folmer RH, Konings RN, & Hilbers CW (1998). Solution structure of the M13 major coat protein in detergent micelles: a basis for a model of phage assembly involving specific residues.
J Mol Biol 282 :401-419.
PubMed Id: 9735296.
doi: 10.1006/jmbi.1998.1860.
Pf1 Major Coat Protein: Pseudomonas phage Pf1  V Viruses, NMR Structure
The structure was determined by solid-state NMR using magnetically aligned bacteriophage particles.
Thiriot et al. (2004).
Thiriot DS, Nevzorov AA, Zagyanskiy L, Wu CH, & Opella SJ (2004). Structure of the coat protein in Pf1 bacteriophage determined by solid-state NMR spectroscopy.
J Mol Biol 341 :869-879.
PubMed Id: 15288792.
doi: 10.1016/j.jmb.2004.06.038.
Pf1 Major Coat Protein in lipid bilayers: Pseudomonas phage Pf1  V Viruses, NMR Structure
Park et al. (2010).
Park SH, Marassi FM, Black D, & Opella SJ (2010). Structure and dynamics of the membrane-bound form of Pf1 coat protein: implications of structural rearrangement for virus assembly.
Biophys J 99 :1465-1474.
PubMed Id: 20816058.
doi: 10.1016/j.bpj.2010.06.009.
fd bacteriophage pVIII coat protein in lipid bilayers: Enterobacteria phage fd  V Viruses, NMR Structure
Marassi & Opella (2003).
Marassi FM & Opella SJ (2003). Simultaneous assignment and structure determination of a membrane protein from NMR orientational restraints.
Protein Sci 12 :403-411.
PubMed Id: 12592011.
doi: 10.1110/ps.0211503.
fd bacteriophage pVIII coat protein in SDS micelles: Enterobacteria phage fd  V Viruses, NMR Structure
Almeida & Opella (1997).
Almeida FC & Opella SJ (1997). fd coat protein structure in membrane environments: structural dynamics of the loop between the hydrophobic trans-membrane helix and the amphipathic in-plane helix.
J Mol Biol 270 :481-495.
PubMed Id: 9237913.
doi: 10.1006/jmbi.1997.1114.
HIV-1 Envelope spike (Env) protein: Human immunodeficiency virus 1  V Viruses (expressed in E. coli), NMR structure
Reconstituted in bicelles. Well-ordered trimer.
Dev et al. (2016).
Dev J, Park D, Fu Q, Chen J, Ha HJ, Ghantous F, Herrmann T, Chang W, Liu Z, Frey G, Seaman MS, Chen B, & Chou JJ (2016). Structural basis for membrane anchoring of HIV-1 envelope spike.
Science 353 :172-175.
PubMed Id: 27338706.
doi: 10.1126/science.aaf7066.
Glycoproteins
Glycophorin A (GpA) transmembrane-domain dimer: Homo sapiens  E Eukaryota (expressed in E. coli), NMR Structure
GpA in dodecylphosphocholine micelles.
MacKenzie et al. (1997).
MacKenzie KR, Prestegard JH, & Engelman DM (1997). A transmembrane helix dimer: structure and implications.
Science 276 :131-133.
PubMed Id: 9082985.
Glycophorin A (GpA) transmembrane-domain dimer: Homo sapiens  E Eukaryota (expressed in E. coli), NMR structure
GpA in DMPC/DHPC bicelles.
in DPC micelles, 2KPE
Mineev et al. (2011).
Mineev KS, Bocharov EV, Volynsky PE, Goncharuk MV, Tkach EN, Ermolyuk YS, Schulga AA, Chupin VV, Maslennikov IV, Efremov RG, & Arseniev AS (2011). Dimeric structure of the transmembrane domain of glycophorin a in lipidic and detergent environments.
Acta Naturae 3 2:90-98.
PubMed Id: 22649687.
Glycophorin A (GpA) transmembrane-domain dimer: Homo sapiens  E Eukaryota (expressed in E. coli), 2.81 Å
Type 1 Lipidic cubic phase crystals showing GpA in bilayer environment
Trenker et al. (2015).
Trenker R, Call ME, & Call MJ (2015). Crystal Structure of the Glycophorin A Transmembrane Dimer in Lipidic Cubic Phase.
J Am Chem Soc 137 50:15676-15679.
PubMed Id: 26642914.
doi: 10.1021/jacs.5b11354.
High-Density Lipoprotein (HDL) Receptors
C-terminal transmembrane domain of scavenger receptor BI (SR-BI): Mus musculus  E Eukaryota (expressed in E. coli), NMR structure
The C-terminal domain contains a leucine zipper dimerization motif
Chadwick et al. (2017).
Chadwick AC, Jensen DR, Hanson PJ, Lange PT, Proudfoot SC, Peterson FC, Volkman BF, & Sahoo D (2017). NMR Structure of the C-Terminal Transmembrane Domain of the HDL Receptor, SR-BI, and a Functionally Relevant Leucine Zipper Motif.
Structure 25 :446-457.
PubMed Id: 28162952.
doi: 10.1016/j.str.2017.01.001.
Tumor Necrosis Factor (TNF) Receptor Superfamily
p75 neurotrophin receptor transmembrane domain: Rattus norvegicus  E Eukaryota (expressed in E. coli), NMR structure
Structure determined in DPC micelles. The transmembrane domain includes residues 245-284 from the complete receptor.
C257A mutant, 2MJO
Nadezhdin et al. (2016).
Nadezhdin KD, García-Carpio I, Goncharuk SA, Mineev KS, Arseniev AS, & Vilar M (2016). Structural Basis of p75 Transmembrane Domain Dimerization.
J Biol Chem 291 23:12346-12357.
PubMed Id: 27056327.
doi: 10.1074/jbc.M116.723585.
Receptor Tyrosine Kinase (RTK) Family
Single-span TM proteins important in cellular signalling
Insulin receptor TM domain (AAs 940-980): Homo sapiens  E Eukaryota (expressed in E. coli), NMR Structure
Li et al. (2014).
Li Q, Wong YL, & Kang C (2014). Solution structure of the transmembrane domain of the insulin receptor in detergent micelles.
Biochim Biophys Acta 1838 :1313-1321.
PubMed Id: 24440425.
doi: 10.1016/j.bbamem.2014.01.005.
Epidermal Growth Factor Receptors (EGFRs)
ErbB (or HER) family of receptor tyrosine kinases (RTKs)
ErbB2 transmembrane segment dimer: Homo sapiens  E Eukaryota (expressed in E. coli), NMR Structure
TM fragment 641-684 of ErbB2 gene. Structure determined in DMPC/DHPC bicelles.
Bocharov et al. (2008).
Bocharov EV, Mineev KS, Volynsky PE, Ermolyuk YS, Tkach EN, Sobol AG, Chupin VV, Kirpichnikov MP, Efremov RG, & Arseniev AS (2008). Spatial structure of the dimeric transmembrane domain of the growth factor receptor ErbB2 presumably corresponding to the receptor active state.
J Biol Chem 283 :6950-6956.
PubMed Id: 18178548.
doi: 10.1074/jbcM709202200.
ErbB2 (HER2) transmembrane segment dimer with juxtamembrane region: Homo sapiens  E Eukaryota (expressed in E. coli), NMR structure
in DPC micelles
Bragin et al. (2016).
Bragin PE, Mineev KS, Bocharova OV, Volynsky PE, Bocharov EV, & Arseniev AS (2016). HER2 Transmembrane Domain Dimerization Coupled with Self-Association of Membrane-Embedded Cytoplasmic Juxtamembrane Regions.
J Mol Biol 428 :52-61.
PubMed Id: 26585403.
doi: 10.1016/j.jmb.2015.11.007.
ErbB1/ErbB2 transmembrane segment heterodimer: Homo sapiens  E Eukaryota (expressed in E. coli), NMR Structure
TM fragment 634-677 of ErbB1 gene. TM fragment 641-685 of ErbB2 gene. Structure determined in DMPC/DHPC bicelles.
Mineev et al. (2010).
Mineev KS, Bocharov EV, Pustovalova YE, Bocharova OV, Chupin VV, & Arseniev AS (2010). Spatial structure of the transmembrane domain heterodimer of ErbB1 and ErbB2 receptor tyrosine kinases.
J Mol Biol 400 :231-243.
PubMed Id: 20471394.
doi: 10.1016/j.jmb.2010.05.016.
ErbB1 transmembrane segment homodimer: Homo sapiens  E Eukaryota (expressed in E. coli), NMR structure
Bocharov et al. (2017).
Bocharov EV, Bragin PE, Pavlov KV, Bocharova OV, Mineev KS, Polyansky AA, Volynsky PE, Efremov RG, & Arseniev AS (2017). The Conformation of the Epidermal Growth Factor Receptor Transmembrane Domain Dimer Dynamically Adapts to the Local Membrane Environment.
Biochemistry 56 12:1697-1705.
PubMed Id: 28291355.
doi: 10.1021/acs.biochem.6b01085.
ErbB3 transmembrane segment dimer: Homo sapiens  E Eukaryota (expressed in E. coli), NMR Structure
TM fragment 639-667 of ErbB3 gene. Structure determined in DPC micelles.
Mineev et al. (2011).
Mineev KS, Khabibullina NF, Lyukmanova EN, Dolgikh DA, Kirpichnikov MP, & Arseniev AS (2011). Spatial structure and dimer--monomer equilibrium of the ErbB3 transmembrane domain in DPC micelles.
Biochim Biophys Acta 1808 :2081-2088.
PubMed Id: 21575594.
doi: 10.1016/j.bbamem.2011.04.017.
ErbB4 transmembrane segment dimer: Homo sapiens  E Eukaryota (expressed in E. coli), NMR Structure
TM fragment 651-678 of ErbB4 gene. Structure determined in DMPC/DHPC bicelles.
Bocharov et al. (2012).
Bocharov EV, Mineev KS, Goncharuk MV, & Arseniev AS (2012). Structural and thermodynamic insight into the process of "weak" dimerization of the ErbB4 transmembrane domain by solution NMR.
Biochim Biophys Acta 1818 :2158-2170.
PubMed Id: 22579757.
doi: 10.1016/j.bbamem.2012.05.001.
Erythropoietin-Producing Hepatocellular Receptors
Eph family of receptor tyrosine kinases (RTKs)
EphA1 transmembrane segment dimer, pH 6.3: Homo sapiens  E Eukaryota (expressed in E. coli), NMR Structure
TM fragment 536-573 of EphA1 gene. Structure determined in DMPC/DHPC bicelles.
Structure at pH 4.3: 2K1K
Bocharov et al. (2008).
Bocharov EV, Mayzel ML, Volynsky PE, Goncharuk MV, Ermolyuk YS, Schulga AA, Artemenko EO, Efremov RG, & Arseniev AS (2008). Spatial structure and pH-dependent conformational diversity of dimeric transmembrane domain of the receptor tyrosine kinase EphA1.
J Biol Chem 283 :29385-29395.
PubMed Id: 18728013.
doi: 10.1074/jbc.M803089200.
EphA2 transmembrane segment dimer: Homo sapiens  E Eukaryota (expressed in E. coli), NMR Structure
TM fragment 523-563 of EphA2 gene. Structure determined in DMPC/DHPC bicelles.
Bocharov et al. (2010).
Bocharov EV, Mayzel ML, Volynsky PE, Mineev KS, Tkach EN, Ermolyuk YS, Schulga AA, Efremov RG, & Arseniev AS (2010). Left-handed dimer of EphA2 transmembrane domain: Helix packing diversity among receptor tyrosine kinases.
Biophys J 98 :881-889.
PubMed Id: 20197042.
doi: 10.1016/j.bpj.2009.11.008.
Fibroblast Growth Factor Receptors
FGFR family of receptor tyrosine kinases (RTKs)
FGFR3 Fibroblast growth factor receptor 3 transmembrane dimer: Homo sapiens  E Eukaryota (expressed in E. coli), NMR Structure
Bocharov et al. (2013).
Bocharov EV, Lesovoy DM, Goncharuk SA, Goncharuk MV, Hristova K, & Arseniev AS (2013). Structure of FGFR3 Transmembrane Domain Dimer: Implications for Signaling and Human Pathologies.
Structure 21 :2087-2093.
PubMed Id: 24120763.
doi: 10.1016/j.str.2013.08.026.
Vascular Endothelial Growth Factor Receptors
VEGFR family of receptor tyrosine kinases (RTKs)
VEGFR2 vascular endothelial growth factor receptor 2 transmembrane dimer: Homo sapiens  E Eukaryota (expressed in E. coli), NMR Structure
TM fragment residues 759-795. Structure determined in DPC micelles.
V769E trimeric mutant: 2MET
G770E/F777E dimeric mutant: 2MEU
Manni et al. (2014).
Manni S, Mineev KS, Usmanova D, Lyukmanova EN, Shulepko MA, Kirpichnikov MP, Winter J, Matkovic M, Deupi X, Arseniev AS, & Ballmer-Hofer K (2014). Structural and functional characterization of alternative transmembrane domain conformations in VEGF receptor 2 activation.
Structure 22 8:1077-1089.
PubMed Id: 24980797.
doi: 10.1016/j.str.2014.05.010.
Integrin Adhesion Receptors
Human Integrin αIIbβ3 transmembrane-cytoplasmic heterodimer: Homo sapiens  E Eukaryota (expressed in E. coli), NMR Structure
Yang et al. (2009).
Yang J, Ma YQ, Page RC, Misra S, Plow EF, & Qin J (2009). Structure of an integrin αIIbβ3 transmembrane-cytoplasmic heterocomplex provides insight into integrin activation.
Proc Natl Acad Sci U S A 106 :17729-17734.
PubMed Id: 19805198.
Adiponectin Receptors
7TM receptors with inverted topology relative to GPCR receptors
Adiponectin is a protein hormone that is important in glucose & fatty acid metabolism
AdipoR1 adiponectin 1 receptor in complex with an Fv fragment: Homo sapiens  E Eukaryota (expressed in Trichoplusia ni), 2.90 Å
This protein and AdipoR2 enclose a large cavity where 3 His residues coördinate a Zn ion.
AdipoR2 adiponectin 2 receptor in complex with Fv fragment, 2.40 Å: 3WXW
Tanabe et al. (2015).
Tanabe H, Fujii Y, Okada-Iwabu M, Iwabu M, Nakamura Y, Hosaka T, Motoyama K, Ikeda M, Wakiyama M, Terada T, Ohsawa N, Hato M, Ogasawara S, Hino T, Murata T, Iwata S, Hirata K, Kawano Y, Yamamoto M, Kimura-Someya T, Shirouzu M, Yamauchi T, Kadowaki T, & Yokoyama S (2015). Crystal structures of the human adiponectin receptors.
Nature 520 7547:312-316.
PubMed Id: 25855295.
doi: 10.1038/nature14301.
AdipoR1 adiponectin 1 receptor in complex with an Fv fragment: Homo sapiens  E Eukaryota (expressed in Trichoplusia ni), 2.73 Å
*5LXG supersedes 3WXV.
AdipoR2 adiponectin 2 receptor in complex with Fv fragment, 2.4 Å: 5LWY
*5LWY supersedes 3WXW
AdipoR2 in complex with a C18 free fatty acid, 2.4 Å: 5LX9
AdipoR2 in complex with a C18 free fatty acid, 3.0 Å: 5LXA
Vasiliauskaité-Brooks et al. (2017).
Vasiliauskaité-Brooks I, Sounier R, Rochaix P, Bellot G, Fortier M, Hoh F, De Colibus L, Bechara C, Saied EM, Arenz C, Leyrat C, & Granier S (2017). Structural insights into adiponectin receptors suggest ceramidase activity.
Nature 544 :120-123.
PubMed Id: 28329765.
doi: 10.1038/nature21714.
G Protein-Coupled Receptors (GPCRs)
Wikipedia Entry
GPCRdb Home Page
GPCR Network Home Page
Rhodopsin: Bos taurus (Bovine) Rod Outer Segment  E Eukaryota, 2.80 Å
See also 1HZX and RPE65 retinoid isomerase
Palczewski et al. (2000).
Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Le Trong I, Teller DC, Okada T, Stenkamp RE, Yamamoto M, & Miyano M (2000). Crystal structure of rhodopsin: A G protein-coupled receptor.
Science 289 :739-745.
PubMed Id: 10926528.
Rhodopsin: Bos taurus (Bovine) Rod Outer Segment  E Eukaryota, 2.6 Å
Okada et al. (2002).
Okada T, Fujiyoshi Y, Silow M, Navarro J, Landau EM, & Shichida Y (2002). Functional role of internal water molecules in rhodopsin revealed by X-ray crystallography.
Proc Natl Acad Sci U S A 99 :5982-5987.
PubMed Id: 11972040.
Rhodopsin, activated state (metarhodopsin II): Bos taurus  E Eukaryota, NMR structure
Choi et al. (2002).
Choi G, Landin J, Galan JF, Birge RR, Albert AD, & Yeagle PL (2002). Structural studies of metarhodopsin II, the activated form of the G-protein coupled receptor, rhodopsin.
Biochemistry 41 :7318-7324.
PubMed Id: 12044163.
Rhodopsin: Bos taurus (Bovine) Rod Outer Segment  E Eukaryota, 2.65 Å
Li et al. (2004).
Li J, Edwards PC, Burghammer M, Villa C, & Schertler GF (2004). Structure of bovine rhodopsin in a trigonal crystal form.
J Mol Biol. 343 :511-521.
PubMed Id: 15491621.
Rhodopsin: Bos taurus  E Eukaryota, 2.65 Å
Alternative model for 1GZM. Described using spacegroup P6 4
Stenkamp (2008).
Stenkamp RE (2008). Alternative models for two crystal structures of bovine rhodopsin.
Acta Crystallogr D Biol Crystallogr D64 :902-904.
PubMed Id: 18645239.
doi: 10.1107/S0907444908017162.
Rhodopsin: Bos taurus (Bovine) Rod Outer Segment  E Eukaryota, 2.2 Å
Okada et al. (2004).
Okada T, Sugihara M, Bondar AN, Elstner M, Entel P, & Buss V (2004). The retinal conformation and its environment in rhodopsin in light of a new 2.2 Å crystal structure.
J Mol Biol 342 :571-583.
PubMed Id: 15327956.
Rhodopsin: Bos taurus (Bovine) Rod Outer Segment  E Eukaryota (expressed in COS cells), 3.4 Å
Recombinant rhodopsin mutant, N2C/D282C
Standfuss et al. (2007).
Standfuss J, Xie G, Edwards PC, Burghammer M, Oprian DD, & Schertler GF (2007). Crystal structure of a thermally stable rhodopsin mutant.
J Mol Biol 372 :1179-1188.
PubMed Id: 17825322.
Rhodopsin: Bos taurus  E Eukaryota, 3.40 Å
Recombinant rhodopsin mutant, N2C/D282C. Refinement of 2J4Y using P6 4 subgroup.
Stenkamp (2008).
Stenkamp RE (2008). Alternative models for two crystal structures of bovine rhodopsin.
Acta Crystallogr D Biol Crystallogr D64 :902-904.
PubMed Id: 18645239.
doi: 10.1107/S0907444908017162.
Rhodopsin, photoactivated: Bos taurus (Bovine) Rod Outer Segment  E Eukaryota, 4.15 Å
Ground state, rhombohedral crystals, 3.8 Å 2I35.
Ground state, trigonal crystals, 4.1 Å 2I36.