Welcome to MPtopo, a curated database of membrane proteins with experimentally validated transmembrane (TM) segments. If you publish work that used MPtopo, please cite Jayasinghe et al. (2001) Protein Sci. 10:455-458.

MPtopo has now been integrated with mpstruc. Unlike the previous version, MPtopo now includes only proteins of known 3D structure; the 1D_Helix entries, whose TM helices were identified by experimental techniques such as gene fusion, have been removed.

MPtopo Querier is no longer available as a separate application, but does remain integral to MPEx. The 'text search' below is similar to 'text search' in mpstruc. We will eventually add additional search capabilities found in the old MPtopo Querier. In addition, we will provide the same capabilities found on the mpstruc page, such as XML representations.

MPtopo currently contains a total of 165 proteins with 949 TM segments.

Latest new protein topology entered: 07 Feb 2007 at 00:00 PST.
Last MPtopo database update: 19 Jul 2013 at 15:14 PDT

Summary of MPtopo Data*
Characteristic Beta-Barrel TM Proteins Alpha-Helical TM Proteins
*Not included in this table (but included in the database) are monotopic proteins and proteins with complex topologies, such as chloride channels, whose TM segments are not easily classified. A list of these proteins is available here (coming soon).
Number of  Proteins/Protein Subunits 25 119
Number of  total residues 10319 27430
Number of residues in TM segments 4207 11848
Number of  total TM segments 334 455
Average TM segment length 12±3 26±5
TM segment length range 6-23 10-48
 
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.

http://blanco.biomol.uci.edu/mpstruc/mptopo/mptopoTblXml
http://blanco.biomol.uci.edu/mpstruc/mptopo/mptopoMonotopicTblXml
http://blanco.biomol.uci.edu/mpstruc/mptopo/mptopoBetaBrlTblXml
http://blanco.biomol.uci.edu/mpstruc/mptopo/mptopoAlphaHlxTblXml

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 includes the following Document Type Definition (DTD):

<!DOCTYPE mptopo [
  <!ELEMENT mptopo (caption,groups*)>
  <!ATTLIST mptopo createdBy CDATA #REQUIRED>
  <!ATTLIST mptopo maintainedBy CDATA #REQUIRED>
  <!ATTLIST mptopo copyright CDATA #REQUIRED>
  <!ATTLIST mptopo url CDATA #REQUIRED>
  <!ATTLIST mptopo lastNewMptopoProteinDate CDATA #REQUIRED>
  <!ATTLIST mptopo lastDatabaseEditDate CDATA #REQUIRED>
  <!ATTLIST mptopo timeStamp CDATA #REQUIRED>
  <!ELEMENT caption (#PCDATA)>
  <!ELEMENT groups (group*)>
  <!ELEMENT group (name,mptopoProteins?,subgroups)>
  <!ELEMENT subgroups (subgroup*)>
  <!ELEMENT subgroup (name,mptopoProteins)>
  <!ELEMENT name (#PCDATA)>
  <!ELEMENT mptopoProteins (mptopoProtein*)>
  <!ELEMENT mptopoProtein (proteinName,species,remarks,pirNumber,
                           uniprotEntry,uniprotNumber,uniprotGene,uniprotName,
                           pdbTitle,pdbCodes,
                           nTerminal,sequence,tmSegments,
                           bibliography,secondaryBibliographies)>
  <!ELEMENT proteinName (#PCDATA)>
  <!ELEMENT species (#PCDATA)>
  <!ELEMENT remarks (#PCDATA)>
  <!ELEMENT pirNumber (#PCDATA)>
  <!ELEMENT uniprotEntry (#PCDATA)>
  <!ELEMENT uniprotNumber (#PCDATA)>
  <!ELEMENT uniprotGene (#PCDATA)>
  <!ELEMENT uniprotName (#PCDATA)>
  <!ELEMENT pdbTitle (#PCDATA)>
  <!ELEMENT pdbCodes (pdbCode*)>
  <!ELEMENT pdbCode (#PCDATA)>
  <!ELEMENT nTerminal (#PCDATA)>
  <!ELEMENT sequence (#PCDATA)>
  <!ELEMENT tmSegments (tmSegment*)>
  <!ELEMENT tmSegment (segLabel,beginIndex,endIndex)>
  <!ELEMENT segLabel (#PCDATA)>
  <!ELEMENT beginIndex (#PCDATA)>
  <!ELEMENT endIndex (#PCDATA)>
  <!ELEMENT bibliography (pubMedId,authors,year,title,journal,volume,issue,pages,doi,notes)>
  <!ELEMENT pubMedId (#PCDATA)>
  <!ELEMENT authors (#PCDATA)>
  <!ELEMENT year (#PCDATA)>
  <!ELEMENT title (#PCDATA)>
  <!ELEMENT journal (#PCDATA)>
  <!ELEMENT volume (#PCDATA)>
  <!ELEMENT issue (#PCDATA)>
  <!ELEMENT pages (#PCDATA)>
  <!ELEMENT doi (#PCDATA)>
  <!ELEMENT notes (#PCDATA)>
  <!ELEMENT secondaryBibliographies (bibliography*)>
]>

 
Membrane Protein Topology Database
Protein
UniProt ID PDB ID Reference
(links are to PubMed)
MONOTOPIC MEMBRANE PROTEINS
prostaglandin synthase-1 (COX-1)* (sheep)
*Monotopic membrane protein that binds on the membrane surface. 'tmsegs' denotes surface-binding helices. Protein is located in ER lumen. Sequence below is from Swiss-Prot. TMhelices=0.

P05979
Picot et al. (1994).
Picot D, Loll PJ, & Garavito RM (1994). The x-ray crystal structure of the membrane protein prostaglandin H2synthase-1.
Nature 367:243-249.
PubMed Id: 8121489.
prostaglandin synthase-2 (COX-2)* (Mus musculus)
*Monotopic membrane protein that binds to the membrane. 'tmsegs' denotes surface-binding helices. Protein is located in the ER lumen. Sequence is processed sequence from Swiss-Prot (17 AA signal sequence removed). TMhelices=0.

Q05769
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.
squalene-hopene cyclase* (Alicyclobacillus acidocaldarius)
*Monotopic membrane protein that binds to membrane surface. 'tmsegs' below indicates helices that interact with the membrane surface. Sequence is from PDB. It differs from Swiss-Prot by the addition Met1. TMhelices=0.

P33247
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.
Monoamine oxidase B* (human)
Monotopic membrane protein because it binds to the membrane surface by a short helix anchor and surface interactions. Sequence is from PDB. It differs from Swiss-Prot by addition of Met1. TMhelices=0.

P27338
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.
fatty acid amide hydrolase* (Rattus norvegicus)
Monotopic membrane protein. Although this protein has a single transmembrane segment (tmseg A), it is classified as monotopic because the active site is external to the membrane. The binding of the protein to membranes is unaffected by removal of tmseg A. 'tmseg' B below refers to a helix-turn-helix motif that causes tight membrane association. Sequence is from Swiss-Prot. TMhelices=1.

P97612
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.
TRANSMEMBRANE PROTEINS: BETA-BARREL
porin (R. capsulatus)
Trimeric beta-barrel. Stands=16. Sequence from Swiss-Prot.

P31243
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.
outer membrane porin (R. blastica)
Trimeric beta-barrel. Strands=16. Sequence from Swiss-Prot.

P39767
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.
OmpK36 osmoporin* (Klebsiella pneumoniae)
*The first (A*) and 17th (*A) 'tmsegs' abut to form a single strand. Trimeric beta-barrel. Strands=16. Sequence is processed sequence from Swiss-Prot (21 AA signal sequence removed).

Q48473
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 (Comamonas acidovorans)
Trimeric beta-barrel. Strands=16. Periplasm = in. Sequence from Swiss-Prot is processed form (19 AA signal sequence removed).

P24305
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.
OmpF porin* (E. coli)
*TM seg. A* (1-6) joins with C-terminus of TM seg. *A (331-340) to form a complete segment. Trimeric beta-barrel. Strands=16. Nterm in = periplasm. Sequence shown is the processed sequence from Swiss-Prot, which is the same as the sequence in the PDB file. Topology & strand assignments are virtually identical to PhoE.

P02931
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.
PhoE phosphoporin* (E. coli)
Trimeric beta-barrel. Nterm in = periplasm. Strands=16. Sequence shown is the processed sequence from Swiss-Prot, which is the same as the sequence in the PDB file. TM seg. A* (1-6) joins with C-terminus of TM seg. *A (324-330) to form a complete segment. Topology & strand assignments are virtually identical to OmpF.

P02932
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.
maltoporin (S. typhimurium)
Trimeric beta-barrel. Strands=18. Nterm in = periplasm. Sequence shown is the processed sequence from Swiss-Prot (25 AA signal sequence removed), which is the same as the sequence in the PDB file.

P26466
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.
maltoporin (E. coli)
Trimeric beta-barrel. Strands=18. Nterm in = periplasm. Sequence shown is processed sequence from Swiss-Prot (25 AA signal sequence removed), which is the same as sequence in PDB file. Related RM# 13837.

P02943
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.
porin scrY, sucrose-specific (S. typhimurium)
Trimeric beta-barrel. Strands=18. Sequence from Swiss-Prot with leader sequence (22 AA) removed. Periplasm = in.

P22340
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 (Mycobacterium smegmatis)
Homooctameric beta-barrel porin. Strands=16 for octamer. TMsegs below are for a monomer. in=periplasm. Sequence is from TrEMBL. The 27AA presequence has been removed.

Q9RLP7
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.
OprP (Pseudomonas aeruginosa)
16-stranded beta-barrel. Trimeric form. Sequence for monomer from PDB file. Sequence in Swiss-Prot has additional 29 aa at the beginning as a signal sequence. There is no signal sequence in PDB file. Thus res#1 in PDB file corresponds to res#30 in Swiss-Prot file.

P05695
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.
outer membrane protein TolC* (Escherichia coli)
*Trimeric beta-barrel transmembrane domain. Strands=4. Sequence and strands shown for one monomer. Sequence below is the processed sequence from Swiss-Prot (22 AA signal sequence removed).

P02930
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.
vitamin B12 receptor (E. coli)
Monomeric beta barrel. Strands=22. Sequence is from Swiss-Prot. The leader sequence (residues 1-20) has been removed in sequence below to correspond to sequence in PDB.

P06129
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.
OmpA (E. coli)
Monomeric beta-barrel. Strands=8. Sequence is processed sequence from Swiss-Prot (21 AA signal sequence removed).

P0A910
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.
OmpT (Escherichia coli)
Monomeric beta-barrel protein. Strands=10. Sequence below is processed sequence from Swiss-Prot (20 AA signal sequence removed). Periplasm = in.

P09169
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.
OmpW (E. coli)
Monomeric 8-stranded beta-barrel. Sequence from PDB. Sequence in Swiss-Prot has additional 21 aa at the beginning as a signal sequence. There is no signal sequence in PDB file and that is why res#1 in PDB file corresponds to res#22 in Swiss-Prot file

P0A915
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.
OmpX (E. coli)
monomeric beta-barrel. Strands=8. Sequence is processed sequence from Swiss-Prot (23 AA signal sequence removed).

P0A917
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.
outer membrane phospholipase A (E. coli)
Monomeric/Dimeric beta-barrel. Strands=12. Nterm in = periplasm. Sequence is processed Swiss-Prot sequence (20 AA signal sequence removed).

P0A921
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.
OpcA (Neisseria meningitidis)
Monomeric beta-barrel. Strands=10. Processed sequence from TrEMBL (19 AA signal sequence removed).

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.
NspA surface protein A (Neisseria meningitidis)
Monomeric beta-barrel. Sequence is processed sequence from Swiss-Prot (19 AA signal sequence removed). Strands=8.

P96943
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.
PagP (Escherichia coli)
Monomeric beta barrel. Strands=8. PDB sequence truncated by 25 residues. TM segments numbered according to Swiss-Prot CrcA sequence. To get PDB numbering, subtract 25 from CrcA numbering.

P37001
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.
FadL (E. coli)
Monomeric, 14-stranded beta-barrel. N terminus in hatch domain. Sequence from PDB. Sequence in Swiss-Prot file has additional 25 aa at the beginning as a signal sequence. Sequence in PDB doesn't have a signal sequence so res#1 in PDB file corresponds to res#26 in Swiss-Prot file.

P10384
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.
Ferric hydroxamate uptake receptor (E. coli)
Monomeric beta-barrel. Strands=22. Sequence is processed sequence from Swiss-Prot (33 AA signal sequence removed).

P06971
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.
FepA (E. coli)
Monomeric beta-barrel. Strands=22. Sequence is processed sequence from Swiss-Prot (22 AA signal sequence removed).

P05825
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 (E. coli)
Monomeric beta-barrel. Strands=22. Sequence is the processed sequence from Swiss-Prot (33 AA signal sequence removed).

P13036
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.
FptA (Pseudomonas aeruginosa)
22-stranded beta-barrel. Sequence from Swiss-Prot.

P42512
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.
NaIP translocator domain (Neisseria meningitidis)
Monomeric beta-barrel. strands=12. in=periplasm. There is also an alpha-helix but it is buried inside the beta-barrel. Sequence is from PDB file. Sequence is truncated relative to Swiss-Prot and starts at res#777.

Q8GKS5
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.
Hia autotransporter (Haemophilus influenzae)
Homotrimer. Monomer is a 4-stranded beta-barrel with one alpha-helix. The homotrimer thus has 3 alpha-helices burried inside a 12-stranded beta-barrel. Sequence for monomer from Swiss-Prot.

Q48152
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.
alpha-hemolysin (S. aureus)
Heptameric beta-barrel toxin. Strands=2. Processed sequence from Swiss-Prot for monomer is shown (26 AA signal sequence removed), which is the same as sequence in PDB file.

P09616
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.
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
bacteriorhodopsin (H. salinarium)
Sequence below is processed sequence from Swiss-Prot (13 AA signal sequence removed). TMhelices=7.

P02945
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.
halorhodopsin (H. salinarium)
Sequence below is unprocessed sequence from Swiss-Prot. AA numbering in PDB file and in the 'tmseg' assignments correspond to unprocessed sequence. Signal sequence corresponds to first 21 AA. TMhelices=7.

P16102
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.
sensory rhodopsin (Anabaena)
Sequence from PDB

Q8YSC4
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 II (N. pharaonis)
Sequence is from Swiss-Prot. TMhelices=7.

P42196
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 transducer (N. pharaonis)
Sequence from Swiss-Prot. PDB sequence is truncated at N- & C-terminii. TMhelices=2.

P42259
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.
rhodopsin (bovine)
Sequence from Swiss-Prot. TMhelices=7.

P02699
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.
M13 coat protein
S-P differs from PDB sequence at two residue positions. Sequence from PDB. TMhelices=1.

P03618
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.
glycophorin A (human)
Sequence is processed sequence from Swiss-Prot (19 AA signal sequence removed). TMhelices=1.

P02724
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.
KcsA potassium channel* (S. lividans)
*The 'tmsegs' marked below include the so-called pore helix (P) associated with the pore region. 'tmseg' B corresponds to P. TMhelices=2.

Q54397
Doyle et al. (1998).
Doyle DA, Cabral JM, Pfuetzner RA, Kuo AL, Gulbis JM, Cohen SL, Chait BT, & MacKinnon R (1998). The structure of the potassium channel: Molecular basis of K+conduction and selectivity.
Science 280:69-77.
PubMed Id: 9525859.
KvAP potassium channel* (Aeropyrum pernix)
*The KvAP K-channel is complex. Of the 'tm segs' marked below, only tmsegs G and I are tmsegs in the usual sense. The others are associated with the pore helix and the voltage sensor domains. Using terminology from the Jiang et al. paper, the 'tmsegs' below have the following correspondence: A=S1, B=S2, C=S3a, D=S3b, E=S4, F=S4-S5 linker, G=S5, H=P, and I=S6.

Q9YDF8
Jiang et al. (2003).
Jiang Y, Lee A, Chen J, Ruta V, Cadene M, Chait BT, & MacKinnon R (2003). X-ray structure of a voltage-dependent K+channel.
Nature 423:33-41.
PubMed Id: 12721618.
Crystal structures.
MthK K+ channel* (Methanobacterium thermoautotrophicum)
*The 'tmsegs' marked below include the so-called pore-helix (P) associated with the pore region. 'tmseg' B corresponds to P. Sequence from Swiss-Prot. TMhelices=2.

O27564
Jiang et al. (2002).
Jiang Y, Lee A, Chen J, Cadene M, Chait BT, MacKinnon R (2002). Crystal structure and mechanism of a calcium-gated potassium channel.
Nature 417:515-22.
PubMed Id: 12037559.
Crystal structure and mechanism.
KirBac1.1 potassium channel* (Burkholderia pseudomallei)
*The 'tmsegs' marked below include the so-called pore-helix (P) associated with the pore region, and the so-called slide-helix (Sl). For 'tmsegs' below, A corresponds to Sl and C to P. Sequence is from TrEMBL. TMhelices=2.

P83698
Kuo et al (2003).
Kuo A, Gulbis JM, Antcliff JF, Rahman T, Lowe ED, Zimmer J, Cuthbertson J, Ashcroft FM, Ezaki T, & Doyle DA (2003). Crystal structure of the potassium channel KirBac1.1 in the closed state.
Science 300:1922-1926.
PubMed Id: 12738871.
NaK channel, Na+ complex (Bacillus cereus)
Tetrameric form. Sequence for monomer from Swiss_Prot.

Q81HW2
Shi et al. (2006).
Shi N, Ye S, Alam A, Chen L, & Jiang Y (2006). Atomic structure of a Na+- and K+-conducting channel.
Nature 440:570-574.
PubMed Id: 16467789.
MscL mechanosensor channel monomer (M. tuberculosis)
Biological unit is a pentamer. Sequence from Swiss-Prot. TMhelices=2.

P0A5K8
Chang et al. (1998).
Chang G, Spencer RH, Lee AT, Barclay MT, & Rees DC (1998). Structure of the MscL homolog from Mycobacterium tuberculosis: A gated mechanosensitive ion channel.
Science 282:2220-2226.
PubMed Id: 9856938.
MscS mechanosensor channel monomer (E. coli)
Biological unit is a heptamer. Sequence from Swiss-Prot. PDB sequence is truncated relative to Swiss-Prot. TMhelices=3.

P0C0S1
Bass et al. (2002).
Bass RB, Strop P, Barclay M, & Rees DC (2002). Crystal Structure of Escherichia coli MscS, a Voltage-modulated and mechanosensitive channel.
Science 298:1582-1587.
PubMed Id: 12446901.
AChR pore alpha subunit (Torpedo marmorata)
Sequence is from PDB, chain A. There is additional 24 AA as signal sequence in Swiss-Prot. TMhelices=4.

P02711
Miyazawa et al. (2003).
Miyazawa A, Fujiyoshi Y, & Unwin N (2003). Structure and gating mechanism of the acetylcholine receptor pore.
Nature 423:949-955.
PubMed Id: 12827192.
AChR pore beta subunit (Torpedo marmorata)
Sequence is from PDB, chain B. There is additional 24 AA as signal sequence in Swiss-Prot. TMhelices=4.

Q6S3I0
Miyazawa et al. (2003).
Miyazawa A, Fujiyoshi Y, & Unwin N (2003). Structure and gating mechanism of the acetylcholine receptor pore.
Nature 423:949-955.
PubMed Id: 12827192.
AChR pore gamma subunit (Torpedo marmorata)
Sequence is from PDB, chain E. Sequence in PDB has first 16 AA removed relative to Swiss-Prot. TMhelices=4.

Q6S3H9
Miyazawa et al. (2003).
Miyazawa A, Fujiyoshi Y, & Unwin N (2003). Structure and gating mechanism of the acetylcholine receptor pore.
Nature 423:949-955.
PubMed Id: 12827192.
AChR pore delta subunit (Torpedo marmorata)
Sequence is from PDB, chain C. Sequence in PDB has first 21 AA removed relative to Swiss-Prot. TMhelices=4.

Q6S3H8
Miyazawa et al. (2003).
Miyazawa A, Fujiyoshi Y, & Unwin N (2003). Structure and gating mechanism of the acetylcholine receptor pore.
Nature 423:949-955.
PubMed Id: 12827192.
aquaporin 1* (human)
One of the TM segments, C* + *C, is composed of two end-to-end helical segments. The two partial segments are counted as 2 TM segments topologically. Sequence is from Swiss-Prot. TMhelices=6.

P29972
Murata et al. (2000).
Murata K, Mitsuoka K, Hirai T, Walz T, Agre P, Heymann J B, Engel A, & Fujiyoshi Y (2000). Structural determinants of water permeation through aquaporin-1.
Nature 407:599-605.
PubMed Id: 11034202.
aquaporin 1* (bovine)
One of the TM segments, C* + *C, is composed of two end-to-end helical segments. The two partial segments are counted as 2 TM segments topologically. Sequence is from Swiss-Prot. TMhelices=6.

P47865
Sui et al. (2001).
Sui H, Han BG, Lee JK, Walian P, & Jap BK (2001). Structural basis of water-specific transport through the AQP1 water channel.
Nature 414:872-8.
PubMed Id: 11780053.
aquaporin Z* (E. coli)
One of the TM segments, C* + *C, is composed of two end-to-end helical segments. The two partial segments are counted as 2 TM segments topologically. Sequence is from Swiss-Prot. TMhelices=6.

P48838
Savage et al. (2003).
Savage DF, Egea PF, Robles-Colmenares Y, Iii JD, & Stroud RM (2003). Architecture and Selectivity in Aquaporins: 2.5 Å X-Ray Structure of Aquaporin Z.
PLoS Biol 1:334-340.
PubMed Id: 14691544.
Glycerol Channel, GlpF* (E. coli)
One of the TM segments, C* + *C, is composed of two end-to-end helical segments. The two partial segments are counted as 2 TM segments topologically. Sequence from Swiss-Prot. TMhelices=6.

P11244
Fu et al. (2000).
Fu D, Libson A, Miercke LJW, Weitzman C, Nollert P, Krucinski J, & Stroud RM (2000). Structure of a glycerol-conducting channel and the basis for its selectivity.
Science 290:481-486.
PubMed Id: 11039922.
amonia transporter AmtB (E. coli)
Sequence from PDB. Swiss-Prot sequence includes signal sequence (first 22 residues). Sequence below is from PDB and does not include signal sequence, therefore res#1 corresponds to res#23 in Swiss-Prot.

P69681
Khademi et al. (2004).
Khademi S, O'Connell J 3rd, Remis J, Robles-Colmenares Y, Miercke LJ, & Stroud RM (2004). Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 Å.
Science 305:1587-1594.
PubMed Id: 15361618.
SecY complex, alpha subunit (Methanococcus jannaschii)
SecY protein. Cytoplasm = in. Sequence is from Swiss-Prot with Met1 removed so that it corresponds to the sequence in the PDB file. TMhelices=10.

Q60175
van den Berg et al. (2004).
van den Berg B, Clemons WM, Collinson I, Hartmann E, Harrison SC, & Rapoport TA (2004). X-ray structure of a protein-conducting channel.
Nature 427:36-44.
PubMed Id: 14661030.
SecY complex, beta subunit (Methanococcus jannaschii)
SecG protein equivalent. Cytoplasm = in. Sequence from PDB. There is no sequence in Swiss-Prot. TMhelices=1.

van den Berg et al. (2004).
van den Berg B, Clemons WM, Collinson I, Hartmann E, Harrison SC, & Rapoport TA (2004). X-ray structure of a protein-conducting channel.
Nature 427:36-44.
PubMed Id: 14661030.
SecY complex, gamma subunit (Methanococcus jannaschii)
SecE protein. Cytoplasm = in. Sequence from Swiss-Prot, with Met1 removed so that sequence corresponds to that in PDB. TMhelices=1.

Q57817
van den Berg et al. (2004).
van den Berg B, Clemons WM, Collinson I, Hartmann E, Harrison SC, & Rapoport TA (2004). X-ray structure of a protein-conducting channel.
Nature 427:36-44.
PubMed Id: 14661030.
Rhomboid Protease GlpG (Escherichia coli)
Sequence from Swiss-Prot.

GLPG_ECOLI
Wang et al. (2006).
Wang Y, Zhang Y, & Ha Y (2006). Crystal structure of a rhomboid family intramembrane protease.
Nature 444:179-183.
PubMed Id: 17051161.
Rhomboid peptidase (Haemophilus influenzae)
Sequence from Swiss-Prot. TM E is unusual in that it is not fully alpha helical but rather is deformed. check orginal article for details.

P44783
Lemieux et al. (2007).
Lemieux MJ, Fischer SJ, Cherney MM, Bateman KS, & James MNG (2007). The crystal structure of the rhomboid peptidase from Haemophilus influenzae provides insight into intramembrane proteolysis.
Proc Natl Acad Sci USA 104:750-754.
PubMed Id: 17210913.
ClC chloride channel* (S. typhimurium)
*The topology of this protein is complex! The 'tmsegs' are all helical segments buried witin the protein and membrane. Check original papers for details. Sequence is from Swiss-Prot. TMhelices=14 (based on turn reversals).

Q8ZRP8
Dutzler et al. (2002).
Dutzler R, Campbell EB, Cadene M, Chait BT, & MacKinnon R (2002). X-ray structure of a ClC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity.
Nature 415:287-294.
PubMed Id: 11796999.
ClC chloride channel* (E. coli)
*The topology of this protein is complex! The 'tmsegs' are all helical segments buried within the protein and membrane. Check original papers for details. Sequence is from Swiss-Prot. TMhelices=14 (based on turn reversals).

P37019
Dutzler et al. (2002).
Dutzler R, Campbell EB, Cadene M, Chait BT, & MacKinnon R (2002). X-ray structure of a ClC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity.
Nature 415:287-294.
PubMed Id: 11796999.
CorA Mg2+ transporter (Thermotoga maritima)
Pentameric form. Sequence for monomer from PDB. See also later structure 2IUB.

Q9WZ31
Lunin et al. (2006).
Lunin VV, Dobrovetsky E, Khutoreskaya G, Zhang R, Joachimiak A, Doyle DA, Bochkarev A, Maguire ME, Edwards AM, & Koth CM (2006). Crystal structure of the CorA Mg2+transporter.
Nature 440:833-837.
PubMed Id: 16598263.
AcrB multidrug transporter (E. coli)
Sequence from Swiss-Prot. TMhelices=12.

P31224
Murakami et al. (2002).
Murakami S, Nakashima R, Yamashita E, & Yamaguchi A (2002). Crystal structure of bacterial multidrug efflux transporter AcrB.
Nature 419:587-593.
PubMed Id: 12374972.
lactose permease, 3D structure (E. coli)
protein is a mutant:C154G. Sequence is thus from PDB file. TMhelices=12.

P02920
Abramson et al. (2003).
Abramson J, Smirnova I, Kasho V, Verner G, Kaback HR, & Iwata S (2003). Structure and mechanism of the lactose permease of Escherichia coli.
Science 301:610-615.
PubMed Id: 12893935.
glycerol-3-phosphate transporter (E. coli)
sequence is from Swiss-Prot, which differs somewhat from PDB. Sequence numbering in PDB corresponds to Swiss-Prot sequence. TMhelices=12.

P08194
Abramson et al. (2003).
Abramson J, Smirnova I, Kasho V, Verner G, Kaback HR, & Iwata S (2003). Structure and mechanism of the lactose permease of Escherichia coli.
Science 301:610-615.
PubMed Id: 12893935.
multidrug resistance protein EmrD (E.coli)
Sequence from Swiss-Prot

P31442
Yin et al. (2006).
Yin Y, He X, Szewczyk P, Nguyen T, & Chang G. (2006). Structure of the multidrug transporter EmrD from Escherichia coli.
Science 312:741-744.
PubMed Id: 16675700.
Na+_H+_antiporter (E. coli)
Sequence from PDB. TM segment D and K consists two short alpha-Helices

P13738
Hunte et al. (2005).
Hunte C, Screpanti E, Venturi M, Rimon A, Padan E, & Michel H (2005). Structure of a Na(+)/H(+) antiporter and insights into mechanism of action and regulation by pH.
Nature 435:1197-1202.
PubMed Id: 15988517.
ADP/ATP carrier protein* (bovine)
*The helices form a deep, broad cavity lined with polar residues. This means that some of the TM segments are quite polar. Sequence from Swiss-Prot. TMhelices=6.

P02722
Pebay-Peyroula et al. (2003).
Pebay-Peyroula E, Dahout-Gonzalez C, Kahn R, Trezeguet V, Lauquin GJ, & Brandolin G (2003). Structure of mitochondrial ADP/ATP carrier in complex with carboxyatractyloside.
Nature 426:39-44.
PubMed Id: 14603310.
BtuCD ABC transporter, BtuC subunit (Escherichia coli)
TM helix G does not cross the membrane completely. It ends in an extended stretch packed between several other helices. Functional protein has 2 BtuC subunits (membrane spanning) & 2 BtuD subunits. Not all TM segments are fully helical. Sequence from Swiss-Prot. TMhelices=10.

Q8X4L7
Locher et al. (2002).
Locher KP, Lee AT, & Rees DC (2002). The E. coli BtuCD structure: A framework for ABC transporter architecture and mechanism.
Science 296:1091-1098.
PubMed Id: 12004122.
F1F0 ATPsynthase Subunit C (E. coli)
Sequence is from Swiss-Prot. For context of this protein, see 1QO1 (ATP synthase rotary motor). TMhelices=2.

P00844
Girvin et al. (1998).
Girvin ME, Rastogi VK, Abildgaard F, Markley JL, & Fillingame RH (1998). Solution structure of the transmembrane H+-transporting subunit c of the F1F0 ATP synthase.
Biochemistry 37:8817-8824.
PubMed Id: 9636021.
doi:10.1021/bi980511m.
F-type Na+-ATPase Subunit C (Ilyobacter tartaricus)
Homodimer. Sequence for monomer from Swiss-Prot. For context of this protein, see 1QO1 (ATP synthase rotary motor)

Q8KRV3
Meier et al. (2005).
Meier T, Polzer P, Diederichs K, Welte W, & Dimroth P (2005). Structure of the rotor ring of F-type Na-ATPase from Ilyobacter tartaricus.
Science 308:659-662.
PubMed Id: 15860619.
Ca ATPase, SR (rabbit)
helix E protrudes into a soluble domain. Nterm in = cytoplasm, out = SR lumen. Sequence is from Swiss-Prot. PDB sequence is C-terminus truncated/modified. TMhelices=10.

P04191
Toyoshima et al. (2000).
Toyoshima C, Nakasako M, Nomura H, & Ogawa H (2000). Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 Å resolution.
Nature 405:647-655.
PubMed Id: 10864315.
phospholamban pentamer (human)
Sequence from PDB. Sequence is for one monomer in pentamer. Also see 1FJK, 1FJP (cardiac phospholamban from pig)

PPLA_HUMAN
Oxenoid and Chou (2005).
Oxenoid K & Chou JJ (2005). The structure of phospholamban pentamer reveals a channel-like architecture in membranes.
Proc Natl Acad Sci USA 102:10870-10875.
PubMed Id: 16043693.
Metalloenzyme pMMO subunit pmoA (Methylococcus capsulatus)
Homotrimer. Sequence for monomer from Swiss-Prot. This corresponds to chain B in PDB file. 2 TM segments, F and G are not a full TM helices. TM segment F is probably not a helix and TM segment G is only a partial helix.

Q607G3
Lieberman & Rosenzweig (2005).
Lieberman RL & Rosenzweig AC (2005). Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane.
Nature 434:177-181.
PubMed Id: 15674245.
Metalloenzyme pMMO subunit pmoB (Methylococcus capsulatus)
Homotrimer. Sequence for monomer from Swiss-Prot. This corresponds to chain A in PDB file.

Q49104
Lieberman & Rosenzweig (2005).
Lieberman RL & Rosenzweig AC (2005). Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane.
Nature 434:177-181.
PubMed Id: 15674245.
Metalloenzyme pMMO subunit pmoC (Methylococcus capsulatus)
Homotrimer. Sequence for monomer from Swiss-Prot. This corresponds to chain C in PDB file.

O05111
Lieberman & Rosenzweig (2005).
Lieberman RL & Rosenzweig AC (2005). Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane.
Nature 434:177-181.
PubMed Id: 15674245.
nitrate reductase A, NarI membrane anchor (E. coli)
Sequence from Swiss-Prot. TMhelices=5.

P11350
Bertero et al. (2003).
Bertero MG, Rothery RA, Palak M, Hou C, Lim D, Blasco F, Weiner JH, & Strynadka NC (2003). Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A.
Nature Structural Biol 10:681-687.
PubMed Id: 12910261.
NrfH (Desulfovibrio vulgaris)
Sequence from PDB, chain C.

Rodrigues et al. (2006).
Rodrigues ML, Oliveira TF, Pereira AC & Archer M (2006). X-ray structure of the membrane-bound cytochrome c quinol dehydrogenase NrfH reveals novel haem coordination.
EMBO J 25:5951-5960.
PubMed Id: 17139260.
Cysteine Oxidase DsbB (Escherichia coli)
Sequence from Swiss-Prot. This corresponds to chain B in PDB file.

P0A6M2
Inaba et al. (2006).
Inaba K, Murakami S, Suzuki M, Nakagawa A, Yamashita E, Okada K, & Ito K (2006). Crystal structure of the DsbA-DsbB complex reveals a mechanism of disulfide bond generation.
Cell 127:789-801.
PubMed Id: 17110337.
Fumarate Reductase. 15 kD anchor (E. coli)
Chain C in PDB file. Helix A and B connected by very short turns to an interfacial helix (N51-L63). Nterm in = cytoplasm. Sequence from Swiss-Prot. TMhelices=3.

P03805
Iverson et al. (1999).
Iverson TM, Luna-Chavez C, Cecchini G, & Rees DC (1999). Structure of the Escherichia coli fumerate reductase respiratory complex.
Science 284:1961-1966.
PubMed Id: 10373108.
Fumarate Reductase. 13 kD anchor (E. coli)
Chain D in PDB file. Helix A strongly (strangely!) kinked at about Ile26. Nterm in = cytoplasm. Sequence from Swiss-Prot. TMhelices=3.

P03806
Iverson et al. (1999).
Iverson TM, Luna-Chavez C, Cecchini G, & Rees DC (1999). Structure of the Escherichia coli fumerate reductase respiratory complex.
Science 284:1961-1966.
PubMed Id: 10373108.
Fumarate Reductase alpha subunit (W. succinogenes)
Chain C in PDB file. Nterm in = cytoplasm. Sequence from Swiss-Prot. TMhelices=5.

P17413
Lancaster et al. (1999).
Lancaster CRD, Kröger A, Auer M, & Michel H (1999). Structure of fumarate reductase from Wolinella succinogenes at 2.2 Å resolution.
Nature 402:377-385.
PubMed Id: 10586875.
formate dehydrogenase-N, beta chain (E. coli)
Chain B in PDB. Sequence from Swiss-Prot. TMhelices=1.

P24184
Jormakka et al. (2002).
Jormakka M, Tornroth S, Byrne B, & Iwata S (2002). Molecular basis of proton motive force generation: structure of formate dehydrogenase-N.
Science 295:1863-1868.
PubMed Id: 11884747.
formate dehydrogenase-N, gamma chain (E. coli)
Chain C in PDB. Sequence from Swiss-Prot. TMhelices=4.

P24185
Jormakka et al. (2002).
Jormakka M, Tornroth S, Byrne B, & Iwata S (2002). Molecular basis of proton motive force generation: structure of formate dehydrogenase-N.
Science 295:1863-1868.
PubMed Id: 11884747.
succinate dehydrogenase C subunit (Escherichia coli)
Sequence is from Swiss-Prot. TMhelices=3.

P10446
Yankovskaya et al. (2003).
Yankovskaya V, Horsefield R, Törnroth S, Luna-Chavez C, Miyoshi H, Léger C, Byrne B, Cecchini G, & Iwata S (2003). Architecture of succinate dehydrogenase and reactive oxygen species generation.
Science 299:700-704.
PubMed Id: 12560550.
succinate dehydrogenase D subunit (Escherichia coli)
Sequence is from Swiss-Prot. TMhelices=3.

P10445
Yankovskaya et al. (2003).
Yankovskaya V, Horsefield R, Törnroth S, Luna-Chavez C, Miyoshi H, Léger C, Byrne B, Cecchini G, & Iwata S (2003). Architecture of succinate dehydrogenase and reactive oxygen species generation.
Science 299:700-704.
PubMed Id: 12560550.
Mito. Respiratory Complex protein CybL (pig)
Sequence from PDB,chain C. PDB sequence starts from res#4. Assigned TM segments account for this. TM helices correspond to 2L,4L and 5L in the article. No Swiss-Prot file for this protein. Matrix=in.

Sun et al. (2005).
Sun F, Huo X, Zhai Y, Wang A, Xu J, Su D, Bartlam M, & Rao Z (2005). Crystal structure of mitochondrial respiratory membrane protein complex II.
Cell 121:1043-1057.
PubMed Id: 15989954.
Mito. Respiratory protein CybS (pig)
Sequence from PDB, chain D. PDB sequence starts with res#34. Assigned TM segments account for this. TM helices correspond to 1S,2S and 3S in the article. No Swiss-Prot file for this protein. Matrix=in.

Sun et al. (2005).
Sun F, Huo X, Zhai Y, Wang A, Xu J, Su D, Bartlam M, & Rao Z (2005). Crystal structure of mitochondrial respiratory membrane protein complex II.
Cell 121:1043-1057.
PubMed Id: 15989954.
cyto. bc1 complex. Chain C (bovine)
Chain designation is that of PDB. Corresponds to cytochrome b in cited paper. Matrix = in. TMhelices=8.

P00157
Iwata et al. (1998).
Iwata S, Lee JW, Okada K, Lee JK, Iwata M, Rasmussen B, Link TA, Ramaswamy S, & Jap BK (1998). Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1complex.
Science 281:64-71.
PubMed Id: 9651245.
cyto. bc1 complex. Chain D (bovine)
Chain designation is that of PDB. Corresponds to cytochrome C1 in cited paper. Matrix = in. TMhelices=1.

P00125
Iwata et al. (1998).
Iwata S, Lee JW, Okada K, Lee JK, Iwata M, Rasmussen B, Link TA, Ramaswamy S, & Jap BK (1998). Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1complex.
Science 281:64-71.
PubMed Id: 9651245.
cyto. bc1 complex. Chain G (bovine)
Chain designation is that of PDB. Corresponds to subunit 7 of cited reference. Sequence also from PDB file. PIR sequence differs in one position from the PDB and Swiss-Prot sequence. Matrix = in. TMhelices=1.

P13271
Iwata et al. (1998).
Iwata S, Lee JW, Okada K, Lee JK, Iwata M, Rasmussen B, Link TA, Ramaswamy S, & Jap BK (1998). Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1complex.
Science 281:64-71.
PubMed Id: 9651245.
cyto. bc1 complex. Chain J (bovine)
Chain designation is that of PDB. Corresponds to subunit 10 in cited paper. Sequence also from PDB file. PIR sequence equal in length but differs in one residue. Matrix = in. TMhelices=1.

P00130
Iwata et al. (1998).
Iwata S, Lee JW, Okada K, Lee JK, Iwata M, Rasmussen B, Link TA, Ramaswamy S, & Jap BK (1998). Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1complex.
Science 281:64-71.
PubMed Id: 9651245.
cyto. bc1 complex. Chain K (bovine)
Chain designation is that of PDB. Corresponds to subunit II in cited paper. Sequence also from PDB file. PDB and PIR are identical, but the Swiss-Prot sequence differs in 3 positions, 2 in the TM domain. Matrix = in. TMhelices=1.

P07552
Iwata et al. (1998).
Iwata S, Lee JW, Okada K, Lee JK, Iwata M, Rasmussen B, Link TA, Ramaswamy S, & Jap BK (1998). Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1complex.
Science 281:64-71.
PubMed Id: 9651245.
cyto. bc1 complex. Chain E (bovine)
Chain designation is that of PDB. Sequence from PDB, which is highly truncated, at both ends, relative to Swiss-Prot. Corresponds to Rieske protein TM domain. Matrix = in. TMhelices=1.

P13272
Iwata et al. (1998).
Iwata S, Lee JW, Okada K, Lee JK, Iwata M, Rasmussen B, Link TA, Ramaswamy S, & Jap BK (1998). Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1complex.
Science 281:64-71.
PubMed Id: 9651245.
cyt. b6f complex, cyto b6 subunit (Mastigocladus laminosus)
Sequence is from PDB. Thylakoid lumen is defined as 'in'. TMhelices=4.

Kurisu et al. (2003).
Kurisu G, Zhang H, Smith JL, & Cramer WA (2003). Structure of the cytochrome b6f complex of oxygenic photosynthesis: tuning the cavity.
Science 302:1009-1014.
PubMed Id: 14526088.
cyt. b6f complex, subunit IV (Mastigocladus laminosus)
Sequence is from PDB. Thylakoid lumen is defined as 'in'. TMhelices=3.

Kurisu et al. (2003).
Kurisu G, Zhang H, Smith JL, & Cramer WA (2003). Structure of the cytochrome b6f complex of oxygenic photosynthesis: tuning the cavity.
Science 302:1009-1014.
PubMed Id: 14526088.
cyt. b6f complex, cytochrome f (Mastigocladus laminosus)
Sequence is from PDB. Thylakoid lumen is defined as 'in'. TMhelices=1.

Kurisu et al. (2003).
Kurisu G, Zhang H, Smith JL, & Cramer WA (2003). Structure of the cytochrome b6f complex of oxygenic photosynthesis: tuning the cavity.
Science 302:1009-1014.
PubMed Id: 14526088.
cyt. b6f complex, Rieske iron-sulfur protein (Mastigocladus laminosus)
Sequence is from PDB. Thylakoid lumen is defined as 'in'. TMhelices=1.

Kurisu et al. (2003).
Kurisu G, Zhang H, Smith JL, & Cramer WA (2003). Structure of the cytochrome b6f complex of oxygenic photosynthesis: tuning the cavity.
Science 302:1009-1014.
PubMed Id: 14526088.
cyt. b6f complex, PetL (Mastigocladus laminosus)
Sequence is from PDB. Thylakoid lumen is defined as 'in'. TMhelices=1.

Kurisu et al. (2003).
Kurisu G, Zhang H, Smith JL, & Cramer WA (2003). Structure of the cytochrome b6f complex of oxygenic photosynthesis: tuning the cavity.
Science 302:1009-1014.
PubMed Id: 14526088.
cyt. b6f complex, PetM (Mastigocladus laminosus)
Sequence is from PDB. Thylakoid lumen is defined as 'in'. TMhelices=1.

Kurisu et al. (2003).
Kurisu G, Zhang H, Smith JL, & Cramer WA (2003). Structure of the cytochrome b6f complex of oxygenic photosynthesis: tuning the cavity.
Science 302:1009-1014.
PubMed Id: 14526088.
cyt. b6f complex, PetG (Mastigocladus laminosus)
Sequence is from PDB. Thylakoid lumen is defined as 'in'. TMhelices=1.

Kurisu et al. (2003).
Kurisu G, Zhang H, Smith JL, & Cramer WA (2003). Structure of the cytochrome b6f complex of oxygenic photosynthesis: tuning the cavity.
Science 302:1009-1014.
PubMed Id: 14526088.
cyt. b6f complex, PetN (Mastigocladus laminosus)
Sequence is from PDB. Thylakoid lumen is defined as 'in'. TMhelices=1.

Kurisu et al. (2003).
Kurisu G, Zhang H, Smith JL, & Cramer WA (2003). Structure of the cytochrome b6f complex of oxygenic photosynthesis: tuning the cavity.
Science 302:1009-1014.
PubMed Id: 14526088.
cyto. C oxidase. Subunit I (bovine)
Chain A in PDB file. Nterm in = matrix. Sequence from Swiss-Prot. TMhelices=12.

P00396
Tsukihara et al. (1996).
Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, & Yoshikawa S (1996). The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å.
Science 272:1136-1144.
PubMed Id: 8638158.
cyto. C oxidase. Subunit II (bovine)
Chain B in PDB file. Nterm in = matrix. Sequence from Swiss-Prot. TMhelices=2.

P00404
Tsukihara et al. (1996).
Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, & Yoshikawa S (1996). The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å.
Science 272:1136-1144.
PubMed Id: 8638158.
cyto. C oxidase. Subunit III (bovine)
Chain C in PDB file. Nterm in = matrix. Sequence from Swiss-Prot. TMhelices=7.

P00415
Tsukihara et al. (1996).
Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, & Yoshikawa S (1996). The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å.
Science 272:1136-1144.
PubMed Id: 8638158.
cyto. C oxidase. Subunit IV (bovine)
Chain D in PDB file. Nterm in = matrix. Sequence is processed sequence from Swiss-Prot (22 AA signal sequence removed). TMhelices=1.

P00423
Tsukihara et al. (1996).
Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, & Yoshikawa S (1996). The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å.
Science 272:1136-1144.
PubMed Id: 8638158.
cyto. C oxidase. Subunit VIa (bovine)
Chain G in PDB file. Nterm in = matrix. Nterm buried within membrane. Nterm end of helix is 'in'. Sequence is processed sequence from Swiss-Prot (12 AA signal sequence removed). TMhelices=1.

P07471
Tsukihara et al. (1996).
Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, & Yoshikawa S (1996). The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å.
Science 272:1136-1144.
PubMed Id: 8638158.
cyto. C oxidase. Subunit VIc (bovine)
Chain I in PDB file. Nterm in = matrix. Sequence from Swiss-Prot. TMhelices=1.

P04038
Tsukihara et al. (1996).
Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, & Yoshikawa S (1996). The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å.
Science 272:1136-1144.
PubMed Id: 8638158.
cyto. C oxidase. Subunit VIIa (bovine)
Chain J in PDB file. Nterm in = matrix. Sequence is processed sequence from Swiss-Prot (21 AA signal sequence removed). TMhelices=1.

P07470
Tsukihara et al. (1996).
Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, & Yoshikawa S (1996). The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å.
Science 272:1136-1144.
PubMed Id: 8638158.
cyto C oxidase. Subunit VIIb (bovine)
Chain K in PDB file. Nterm in = matrix. Sequence is processed sequence from Swiss-Prot (24 AA signal sequence removed). TMhelices=1.

P13183
Tsukihara et al. (1996).
Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, & Yoshikawa S (1996). The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å.
Science 272:1136-1144.
PubMed Id: 8638158.
cyto. C oxidase. Subunit VIIc (bovine)
Chain L in PDB file. Nterm in = matrix. Sequence is processed sequence from Swiss-Prot (16 AA signal sequence removed). TMhelices=1.

P00430
Tsukihara et al. (1996).
Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, & Yoshikawa S (1996). The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å.
Science 272:1136-1144.
PubMed Id: 8638158.
cyto. C oxidase. Subunit VIII (bovine)
Chain M in PDB file. Nterm in = matrix. Sequence is processed sequence from Swiss-Prot (24 AA signal sequence removed). TMhelices=1.

P10175
Tsukihara et al. (1996).
Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, & Yoshikawa S (1996). The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å.
Science 272:1136-1144.
PubMed Id: 8638158.
cyto. C oxidase. Subunit I (P. denitrificans)
Chain A in PDB file. See also J. Biol. Chem. (1999) 274:33296-33299. Sequence from Swiss-Prot. TMhelices=12.

P98002
Iwata et al. (1995).
Iwata S, Ostermeier C, Ludwig B, & Michel H (1995). Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans.
Nature 376:660-669.
PubMed Id: 7651515.
cyto. C oxidase. Subunit II (P. denitrificans)
Chain B in PDB file. See also J.Biol.Chem. (1999) 274:33296-33299. Nterm in = cytoplasm. Sequence is processed sequence from Swiss-Prot (29 AA signal sequence removed). TMhelices=2.

P08306
Iwata et al. (1995).
Iwata S, Ostermeier C, Ludwig B, & Michel H (1995). Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans.
Nature 376:660-669.
PubMed Id: 7651515.
cyto. C oxidase. Subunit III (P. denitrificans)
Chain C in PDB file. Nterm in = cytoplasm. See also J. Biol. Chem. (1999), 274:33296-33299. Sequence from Swiss Prot. TMhelices=7.

P06030
Iwata et al. (1995).
Iwata S, Ostermeier C, Ludwig B, & Michel H (1995). Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans.
Nature 376:660-669.
PubMed Id: 7651515.
cyto. C oxidase. Subunit IV (P. denitrificans)
Chain D in PDB file. See also J. Biol. Chem. (1999), 274:33296-33299. Sequence from Swiss Prot. TMhelices=1.

P77921
Iwata et al. (1995).
Iwata S, Ostermeier C, Ludwig B, & Michel H (1995). Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans.
Nature 376:660-669.
PubMed Id: 7651515.
cyto.c oxidase. Chain I (Thermus thermophilus)
Chain A in PDB file. Sequence from Swiss-Prot. cytoplasm = in. TMhelices=13.

Q56408
Soulimane et al. (2000).
Soulimane T, Buse G, Bourenkov GP, Bartunik HD, Huber R, & Than ME (2000). Structure and mechanism of the aberrant ba3-cytochrome c oxidase from Thermus thermophilus.
EMBO J 19:1766-1776.
PubMed Id: 10775261.
cyto.c oxidase. Chain II (Thermus thermophilus)
Chain B in PDB file. Sequence from Swiss-Prot. cytoplasm = in. TMhelices=1.

P98052
Soulimane et al. (2000).
Soulimane T, Buse G, Bourenkov GP, Bartunik HD, Huber R, & Than ME (2000). Structure and mechanism of the aberrant ba3-cytochrome c oxidase from Thermus thermophilus.
EMBO J 19:1766-1776.
PubMed Id: 10775261.
cyto.c oxidase. Chain IIa (Thermus thermophilus)
Chain C in PDB file. Sequence is from Swiss-Prot. cytoplasm = in. TMhelices=1.

P82543
Soulimane et al. (2000).
Soulimane T, Than ME, Dewor M, Huber R, & Buse G (2000). Primary structure of a novel subunit in ba3-cytochrome oxidase from Thermus thermophilus.
Protein Sci 9:2068-2073.
PubMed Id: 11152118.
doi:10.1110/ps.9.11.2068.
ubiquinol oxidase subunit I (E. coli)
Sequence is from Swiss-Prot. Helices A & O are not reported in the 1EFT structure file. Their assignments are from Swiss-Prot.

P18401
Abramson et al. (2000).
Abramson J, Riistama S, Larsson G, Jasaitis A, Svensson-Ek M, Laakkonen L, Puustinen A, Iwata S, & Wikstrom M (2000). The structure of the ubiquinol oxidase from Escherichia coli and its ubiquinone binding site.
Nat Struct Biol 7:910-917.
PubMed Id: 11017202.
ubiquinol oxidase subunit II (E. coli)
Sequence is from Swiss-Prot. This corresponds to chain B in PDB file. Although the sequence has a signal sequence, helix numbering is for unprocessed sequence.

P0ABJ1
Abramson et al. (2000).
Abramson J, Riistama S, Larsson G, Jasaitis A, Svensson-Ek M, Laakkonen L, Puustinen A, Iwata S, & Wikstrom M (2000). The structure of the ubiquinol oxidase from Escherichia coli and its ubiquinone binding site.
Nat Struct Biol 7:910-917.
PubMed Id: 11017202.
ubiquinol oxidase subunit III (E. coli)
Sequence from Swiss-Prot.

P18402
Abramson et al. (2000).
Abramson J, Riistama S, Larsson G, Jasaitis A, Svensson-Ek M, Laakkonen L, Puustinen A, Iwata S, & Wikstrom M (2000). The structure of the ubiquinol oxidase from Escherichia coli and its ubiquinone binding site.
Nat Struct Biol 7:910-917.
PubMed Id: 11017202.
photosystem I A subunit (Synechococcus elongatus)
Stroma=in. Sequence from Swiss-Prot. TMhelices=11.

P25896
Jordan et al. (2001).
Jordan P, Fromme P, Witt HT, Klukas O, Saenger W, & Krauss N (2001). Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution.
Nature 411:909-917.
PubMed Id: 11418848.
photosystem I B subunit (Synechococcus elongatus)
Stroma=in. Sequence from Swiss-Prot. TMhelices=11.

P25897
Jordan et al. (2001).
Jordan P, Fromme P, Witt HT, Klukas O, Saenger W, & Krauss N (2001). Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution.
Nature 411:909-917.
PubMed Id: 11418848.
photosystem I F subunit* (Synechococcus elongatus)
*Only helix A is transmembrane. Helix B does not cross the membrane, but is buried in it with a kink so that it enters and leaves from the same side (stromal) of the membrane. Stroma = in. Sequence is the processed sequence from Swiss-Prot (23 AA signal sequence removed).

P0A401
Jordan et al. (2001).
Jordan P, Fromme P, Witt HT, Klukas O, Saenger W, & Krauss N (2001). Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution.
Nature 411:909-917.
PubMed Id: 11418848.
photosystem I I subunit (Synechococcus elongatus)
Stroma=in. Sequence from Swiss-Prot. TMhelices=1.

P25900
Jordan et al. (2001).
Jordan P, Fromme P, Witt HT, Klukas O, Saenger W, & Krauss N (2001). Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution.
Nature 411:909-917.
PubMed Id: 11418848.
photosystem I J subunit (Synechococcus elongatus)
Stroma=in. Sequence from Swiss-Prot. TMhelices=1.

P25901
Jordan et al. (2001).
Jordan P, Fromme P, Witt HT, Klukas O, Saenger W, & Krauss N (2001). Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution.
Nature 411:909-917.
PubMed Id: 11418848.
photosystem I K subunit (Synechococcus elongatus)
Stroma=in. Sequence is unprocessed sequence from Swiss-Prot, which corresponds to AA numbering in PDB file. TMhelices=2.

P20453
Jordan et al. (2001).
Jordan P, Fromme P, Witt HT, Klukas O, Saenger W, & Krauss N (2001). Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution.
Nature 411:909-917.
PubMed Id: 11418848.
photosystem I L subunit (Synechococcus elongatus)
Stroma = in. Sequence is from Swiss-Prot, with Met1 removed in order to agree with AA numbering in PDB file. TMhelices=3.

P25902
Jordan et al. (2001).
Jordan P, Fromme P, Witt HT, Klukas O, Saenger W, & Krauss N (2001). Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution.
Nature 411:909-917.
PubMed Id: 11418848.
photosystem I M subunit (Synechococcus elongatus)
Stroma=in. Sequence from Swiss-Prot. TMhelices=1.

P25903
Jordan et al. (2001).
Jordan P, Fromme P, Witt HT, Klukas O, Saenger W, & Krauss N (2001). Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution.
Nature 411:909-917.
PubMed Id: 11418848.
photosystem I X subunit (Synechococcus elongatus)
Stroma=in. Sequence from TrEMBL. TMhelices=1.

Q8DKP6
Jordan et al. (2001).
Jordan P, Fromme P, Witt HT, Klukas O, Saenger W, & Krauss N (2001). Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution.
Nature 411:909-917.
PubMed Id: 11418848.
Photosystem II Q(B) protein (Thermosynechococcus elongatus)
Sequence from Swiss-Prot. This corresponds to chain A in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.

P0A444
Ferreira et al. (2004).
Ferreira KN, Iverson TM, Maghlaoui K, Barber J, & Iwata S (2004). Architecture of the photosynthetic oxygen-evolving center.
Science 303:1831-1838.
PubMed Id: 14764885.
photosystem II core light harvesting protein (Thermosynechococcus elongatus)
Sequence from Swiss-Prot. This corresponds to chain B in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.

Q8DIQ1
Ferreira et al. (2004).
Ferreira KN, Iverson TM, Maghlaoui K, Barber J, & Iwata S (2004). Architecture of the photosynthetic oxygen-evolving center.
Science 303:1831-1838.
PubMed Id: 14764885.
Photosystem II CP43 protein (Thermosynechococcus elongatus)
Sequence from Swiss-Prot. This corresponds to chain C in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.

Q8DIF8
Ferreira et al. (2004).
Ferreira KN, Iverson TM, Maghlaoui K, Barber J, & Iwata S (2004). Architecture of the photosynthetic oxygen-evolving center.
Science 303:1831-1838.
PubMed Id: 14764885.
Photosystem II D2 protein (Thermosynechococcus elongatus)
Sequence from Swiss-Prot. This corresponds to chain D in PDB file. TM C and E contains of two helices. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.

Q8CM25
Ferreira et al. (2004).
Ferreira KN, Iverson TM, Maghlaoui K, Barber J, & Iwata S (2004). Architecture of the photosynthetic oxygen-evolving center.
Science 303:1831-1838.
PubMed Id: 14764885.
Photosystem II Cytochrome b559 alpha subunit (Thermosynechococcus elongatus)
Sequence from Swiss-Prot. This corresponds to chain E in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.

Q8DIP0
Ferreira et al. (2004).
Ferreira KN, Iverson TM, Maghlaoui K, Barber J, & Iwata S (2004). Architecture of the photosynthetic oxygen-evolving center.
Science 303:1831-1838.
PubMed Id: 14764885.
Photosystem II Cytochrome b559 beta subunit (Thermosynechococcus elongatus)
Sequence from Swiss-Prot. This corresponds to chain F in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.

Q8DIN9
Ferreira et al. (2004).
Ferreira KN, Iverson TM, Maghlaoui K, Barber J, & Iwata S (2004). Architecture of the photosynthetic oxygen-evolving center.
Science 303:1831-1838.
PubMed Id: 14764885.
Photosystem II PsbH protein (Thermosynechococcus elongatus)
Sequence from Swiss-Prot. This corresponds to chain H in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.

Q8DJ43
Ferreira et al. (2004).
Ferreira KN, Iverson TM, Maghlaoui K, Barber J, & Iwata S (2004). Architecture of the photosynthetic oxygen-evolving center.
Science 303:1831-1838.
PubMed Id: 14764885.
Photosystem II PsbI protein (Thermosynechococcus elongatus)
Sequence from Swiss-Prot. This corresponds to chain I in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.

Q8DJZ6
Ferreira et al. (2004).
Ferreira KN, Iverson TM, Maghlaoui K, Barber J, & Iwata S (2004). Architecture of the photosynthetic oxygen-evolving center.
Science 303:1831-1838.
PubMed Id: 14764885.
Photosystem II PsbJ protein (Thermosynechococcus elongatus)
Sequence from Swiss-Prot. This corresponds to chain J in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.

P59087
Ferreira et al. (2004).
Ferreira KN, Iverson TM, Maghlaoui K, Barber J, & Iwata S (2004). Architecture of the photosynthetic oxygen-evolving center.
Science 303:1831-1838.
PubMed Id: 14764885.
Photosystem II PsbK protein (Thermosynechococcus elongatus)
Sequence from PDB, chain K. In Swiss-Prot file there is aditional 9 aa at the beginning so res#1 in PBD file corresponds to res#10 in Swiss-Prot file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.

Q9F1K9
Ferreira et al. (2004).
Ferreira KN, Iverson TM, Maghlaoui K, Barber J, & Iwata S (2004). Architecture of the photosynthetic oxygen-evolving center.
Science 303:1831-1838.
PubMed Id: 14764885.
Photosystem II PsbL protein (Thermosynechococcus elongatus)
Sequence from Swiss-Prot. This corresponds to chain L in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.

Q8DIN8
Ferreira et al. (2004).
Ferreira KN, Iverson TM, Maghlaoui K, Barber J, & Iwata S (2004). Architecture of the photosynthetic oxygen-evolving center.
Science 303:1831-1838.
PubMed Id: 14764885.
Photosystem II PsbM protein (Thermosynechococcus elongatus)
Sequence from Swiss-Prot. This corresponds to chain M in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.

Q8DHA7
Ferreira et al. (2004).
Ferreira KN, Iverson TM, Maghlaoui K, Barber J, & Iwata S (2004). Architecture of the photosynthetic oxygen-evolving center.
Science 303:1831-1838.
PubMed Id: 14764885.
Photosystem II PsbT protein (Thermosynechococcus elongatus)
Sequence from Swiss-Prot. This corresponds to chain T in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.

Q8DIQ0
Ferreira et al. (2004).
Ferreira KN, Iverson TM, Maghlaoui K, Barber J, & Iwata S (2004). Architecture of the photosynthetic oxygen-evolving center.
Science 303:1831-1838.
PubMed Id: 14764885.
Photosystem II PsbX protein (Thermosynechococcus elongatus)
Sequence from Swiss-Prot. This corresponds to chain X in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.

Q8DHE6
Ferreira et al. (2004).
Ferreira KN, Iverson TM, Maghlaoui K, Barber J, & Iwata S (2004). Architecture of the photosynthetic oxygen-evolving center.
Science 303:1831-1838.
PubMed Id: 14764885.
Photosystem II PsbN protein (Thermosynechococcus elongatus)
Sequence from Swiss-Prot. This corresponds to chain N in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.

Q8DJ42
Ferreira et al. (2004).
Ferreira KN, Iverson TM, Maghlaoui K, Barber J, & Iwata S (2004). Architecture of the photosynthetic oxygen-evolving center.
Science 303:1831-1838.
PubMed Id: 14764885.
Photosystem II PsbZ protein (Thermosynechococcus elongatus)
Sequence from Swiss-Prot. This corresponds to chain Z in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.

Q8DHJ2
Ferreira et al. (2004).
Ferreira KN, Iverson TM, Maghlaoui K, Barber J, & Iwata S (2004). Architecture of the photosynthetic oxygen-evolving center.
Science 303:1831-1838.
PubMed Id: 14764885.
Light Harvesting Complex. alpha chain (R. acidophila)
Chain A of PDB file. Sequence from Swiss-Prot. TMhelices=1.

P26789
McDermott et al. (1995)
McDermott G, Prince SM, Freer AA, Hawthornthwaite-Lawless AM, Papiz MZ, Cogdell RJ & Isaacs NW (1995). Crystal structure of an integral membrane light-harvesting complex from photosynthetic bacteria.
Nature 374:517-521.
doi:10.1038/374517a0.
Light Harvesting Complex. beta chain (R. acidophila)
Chain B of PDB file. Sequence from Swiss-Prot. TMhelices=1.

P26790
McDermott et al. (1995)
McDermott G, Prince SM, Freer AA, Hawthornthwaite-Lawless AM, Papiz MZ, Cogdell RJ & Isaacs NW (1995). Crystal structure of an integral membrane light-harvesting complex from photosynthetic bacteria.
Nature 374:517-521.
doi:10.1038/374517a0.
Light Harvesting Complex. alpha chain (R. molischianum)
Chain A of PDB file. Sequence from Swiss-Prot. TMhelices=1.

P97253
Koepke et al. (1996).
Koepke J, Hu XC, Muenke C, Schulten K, & Michel H (1996). The crystal structure of the light-harvesting complex II (B800- 850) from Rhodospirillum molischianum.
Structure 4:581-597.
PubMed Id: 8736556.
Light Harvesting Complex. beta chain (R. molischianum)
Chain B in PDB file. Sequence from Swiss-Prot. TMhelices=1.

P95673
Koepke et al. (1996).
Koepke J, Hu XC, Muenke C, Schulten K, & Michel H (1996). The crystal structure of the light-harvesting complex II (B800- 850) from Rhodospirillum molischianum.
Structure 4:581-597.
PubMed Id: 8736556.
LHC-II (Spinacia oleracea)
Sequence is from Swiss-Prot. The 35AA pre-sequence has been removed, consistent with PDB sequence. Stroma=in.

P12333
Liu et al. (2004).
Liu Z, Yan H, Wang K, Kuang T, Zhang J, Gui L, An X, & Chang W (2004). Crystal structure of spinach major light-harvesting complex at 2.72 Å resolution.
Nature 428:287-292.
PubMed Id: 15029188.
Reaction center. Chain H (R. viridis)
Sequence from Swiss-Prot. TMhelices=1.

P06008
Deisenhofer et al. (1985).
Deisenhofer J, Epp O, Miki K, Huber R, & Michel H (1985). Structure of the protein subunits in the photosynthetic reaction centre of Rhodospeudomonas viridis at 3 Å resolution.
Nature 318:618-624.
PubMed Id: 22439175.
Reaction center. Chain L (R. viridis)
Sequence from Swiss-Prot. TMhelices=5.

P06009
Deisenhofer et al. (1985).
Deisenhofer J, Epp O, Miki K, Huber R, & Michel H (1985). Structure of the protein subunits in the photosynthetic reaction centre of Rhodospeudomonas viridis at 3 Å resolution.
Nature 318:618-624.
PubMed Id: 22439175.
Reaction center. Chain M (R. viridis)
Sequence from Swiss-Prot. TMhelices=5.

P06010
Deisenhofer et al. (1985).
Deisenhofer J, Epp O, Miki K, Huber R, & Michel H (1985). Structure of the protein subunits in the photosynthetic reaction centre of Rhodospeudomonas viridis at 3 Å resolution.
Nature 318:618-624.
PubMed Id: 22439175.
Reaction center. Chain H (R. sphaeroides)
Sequence from Swiss-Prot. TMhelices=1.

P11846
Allen et al. (1987).
Allen JP, Feher G, Yeates TO, Komiya H, & Rees DC (1987). Structure of the reaction center from Rhodobacter sphaeroides R-26: the protein subunits.
Proc Natl Acad Sci USA 84:6162-6166.
PubMed Id: 2819866.
Reaction center. Chain L (R. sphaeroides)
Sequence from Swiss-Prot. TMhelices=5.

P02954
Allen et al. (1987).
Allen JP, Feher G, Yeates TO, Komiya H, & Rees DC (1987). Structure of the reaction center from Rhodobacter sphaeroides R-26: the protein subunits.
Proc Natl Acad Sci USA 84:6162-6166.
PubMed Id: 2819866.
Reaction center. Chain M (R. sphaeroides)
Sequence from Swiss-Prot. TMhelices=5.

P02953
Allen et al. (1987).
Allen JP, Feher G, Yeates TO, Komiya H, & Rees DC (1987). Structure of the reaction center from Rhodobacter sphaeroides R-26: the protein subunits.
Proc Natl Acad Sci USA 84:6162-6166.
PubMed Id: 2819866.
reaction center chain H (Thermochromatium tepidum)
Sequence from PDB. TMhelices=1.

Nogi et al. (2000).
Nogi T, Fathir I, Kobayashi M, Nozawa T, & Miki K (2000). Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: thermostability and electron transfer.
Proc Natl Acad Sci USA 97:6031-6036.
PubMed Id: 11095707.
reaction center chain L (Thermochromatium tepidum)
Sequence from PDB. TMhelices=5

Nogi et al. (2000).
Nogi T, Fathir I, Kobayashi M, Nozawa T, & Miki K (2000). Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: thermostability and electron transfer.
Proc Natl Acad Sci USA 97:6031-6036.
PubMed Id: 11095707.
reaction center chain M (Thermochromatium tepidum)
Sequence from PDB. TMhelices=5.

Nogi et al. (2000).
Nogi T, Fathir I, Kobayashi M, Nozawa T, & Miki K (2000). Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: thermostability and electron transfer.
Proc Natl Acad Sci USA 97:6031-6036.
PubMed Id: 11095707.