SCOPe Funding Alert: SCOPe support from the NIH ended in April 2016. John-Marc Chandonia is the primary maintainer and has continued to develop SCOPe using vacation time. Three proposals to the NIH for continued funding have been unsuccessful. If our current NIH proposal is not funded, SCOPe will shut down permanently in Summer 2017 as Dr. Chandonia will need to seek a new position.

Lineage for Class f: Membrane and cell surface proteins and peptides

  1. Root: SCOPe 2.06
  2. 2223823Class f: Membrane and cell surface proteins and peptides [56835] (59 folds)

Folds:

  1. 2223824f.1: Toxins' membrane translocation domains [56836] (5 superfamilies)
    multi-helical domains of various folds which is thought to unfold in the membrane
  2. 2224181f.3: Light-harvesting complex subunits [56917] (1 superfamily)
    membrane all-alpha fold
  3. 2224301f.4: Transmembrane beta-barrels [56924] (7 superfamilies)
    not a true fold, gathers together transmembrane barrels of different (n,S)
  4. 2224731f.5: Outer membrane efflux proteins (OEP) [56953] (1 superfamily)
    subunit fold contains tandem repeat of alpha-beta hairpin-alpha(2) motif
    trimeric fold contains barrel (n=12, S=18) formed by beta-hairpins, two from each subunit, and a bundle of helices with a channel running through it
  5. 2224772f.6: Leukocidin-like [56958] (1 superfamily)
    subunit fold contains beta-sandwich of Ig-like (grerk-key) topology and a beta-ribbon arm that forms an oligomeric transmembrane barrel
  6. 2224946f.7: Lipovitellin-phosvitin complex; beta-sheet shell regions [56967] (1 superfamily)
    contains several large open beta-sheets
  7. 2224954f.8: Aerolisin/ETX pore-forming domain [56972] (1 superfamily)
    3 domains: (1) alpha+beta; (2&3) all-beta
  8. 2225008f.9: Perfringolysin [56977] (1 superfamily)
    2 domains: (1) alpha+beta; (2) all-beta, similar to the CalB domain fold but the two last strands are transposed
  9. 2225037f.10: Viral glycoprotein, central and dimerisation domains [56982] (1 superfamily)
    2 intertwined domains; all-beta and alpha+beta
  10. 2225103f.12: Head and neck region of the ectodomain of NDV fusion glycoprotein [69921] (1 superfamily)
    3 intertwined all-beta domains
  11. 2225114f.13: Class A G protein-coupled receptor (GPCR)-like [81322] (1 superfamily)
    core: up-and-down bundle of seven transmembrane helices tilted 20 degrees with respect to the plane of the membrane
  12. 2225430f.14: Gated ion channels [81325] (2 superfamilies)
    oligomeric transmembrane alpha-helical proteins
  13. 2225582f.15: Small-conductance potassium channel [81328] (1 superfamily)
    oligomeric transmembrane alpha-helical protein
  14. 2225596f.16: Gated mechanosensitive channel [81331] (1 superfamily)
    oligomeric transmembrane alpha-helical protein
  15. 2225606f.17: Transmembrane helix hairpin [81334] (6 superfamilies)
    two antiparallel transmembrane helices
  16. 2225847f.18: F1F0 ATP synthase subunit A [81337] (1 superfamily)
    core: up-and-down bundle of four transmembrane helices
  17. 2225853f.19: Aquaporin-like [81339] (1 superfamily)
    core: 8 helices, 2 short helices are surrounded by 6 long transmembrane helices
  18. 2225962f.20: Clc chloride channel [81341] (1 superfamily)
    core: 18 transmembrane helices
  19. 2226050f.21: Heme-binding four-helical bundle [81344] (3 superfamilies)
    core: four transmembrane helices, up-and-down bundle, binds one or two heme groups in between the helices
  20. 2226284f.22: ABC transporter involved in vitamin B12 uptake, BtuC [81346] (1 superfamily)
    multihelical; complex architecture with several transmembrane helices
  21. 2226297f.23: Single transmembrane helix [81407] (42 superfamilies)
    not a true fold
  22. 2227563f.24: Cytochrome c oxidase subunit I-like [81443] (1 superfamily)
    12 transmembrane helices in an approximate threefold rotational symmetric arrangement
  23. 2227687f.25: Cytochrome c oxidase subunit III-like [81453] (1 superfamily)
    core: 7 transmembrane helices organized into two bundles, one formed by the first two helices and the other by the rest
  24. 2227758f.26: Bacterial photosystem II reaction centre, L and M subunits [81484] (1 superfamily)
    five transmembrane helices forming a sheet-like structure
  25. 2228048f.27: 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81525] (1 superfamily)
    membrane-associated alpha-helical protein; no transmembrane helices
  26. 2228112f.28: Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81532] (1 superfamily)
    membrane-associated alpha-helical protein; no transmembrane helices
  27. 2228175f.29: Photosystem I subunits PsaA/PsaB [81559] (1 superfamily)
    core:11 transmembrane helices
  28. 2228198f.30: Photosystem I reaction center subunit X, PsaK [81564] (1 superfamily)
    core: hairpin of two transmembrane helices
  29. 2228204f.31: Photosystem I reaction center subunit XI, PsaL [81569] (1 superfamily)
    core: three transmembrane helices, bundle
  30. 2228210f.32: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81649] (1 superfamily)
    core: three transmembrane helices, up-and-down bundle
  31. 2228298f.33: Metal cation-transporting ATPase, transmembrane domain [81666] (1 superfamily)
    core: multihelical; consists of three transmembrane regions of 2, 2 and 6 helices, separated by cytoplasmic domains
  32. 2228376f.34: Mechanosensitive channel protein MscS (YggB), transmembrane region [82860] (1 superfamily)
    oligomeric fold; 3 transmembrane helices per subunit
  33. 2228395f.35: Multidrug efflux transporter AcrB transmembrane domain [82865] (1 superfamily)
    12 transmembrane helices; duplication: the N- and C-terminal halves of the whole proteins are structurally similar
  34. 2228418f.36: Neurotransmitter-gated ion-channel transmembrane pore [90111] (1 superfamily)
    heteropentameric transmembrane alpha-helical protein; 4 transmembrane helices per subunit
  35. 2228434f.37: ABC transporter transmembrane region [90122] (1 superfamily)
    multihelical; complex architecture with several transmembrane helices
  36. 2228466f.38: MFS general substrate transporter [103472] (1 superfamily)
    12 transmembrane helices; duplication: the N- and C-terminal halves are structurally similar
  37. 2228503f.40: V-type ATP synthase subunit C [103485] (1 superfamily)
    9 transmembrane helices
  38. 2228515f.41: Preprotein translocase SecY subunit [103490] (1 superfamily)
    10 transmembrane helices forming of a gated channel
  39. 2228531f.42: Mitochondrial carrier [103505] (1 superfamily)
    membrane all-alpha fold; 6-helical "barrel" with internal binding cavity
  40. 2228546f.43: Chlorophyll a-b binding protein [103510] (1 superfamily)
    membrane all-alpha fold; three transmembrane helices
  41. 2228588f.44: Ammonium transporter [111351] (1 superfamily)
    11 transmembrane helices; duplication: consist of 2 structural repeats of five helices each plus extra C-terminal helix
  42. 2228634f.45: Mitochondrial ATP synthase coupling factor 6 [111356] (1 superfamily)
    2 helices, hairpin
  43. 2228642f.46: HlyD-like secretion proteins [111368] (1 superfamily)
    consists of three domains: beta-barrel (res. 29-38,170-259; (50412)); barrel-sandwich hybrid (39-72,135-169; (51230)) and long alpha-hairpin (73-134; (46556))
  44. 2228682f.47: VP4 membrane interaction domain [111378] (1 superfamily)
    2 domains; d1: complexed all-beta fold; d2: coiled-coil (trimeric) helical region
  45. 2228693f.48: OmpH-like [111383] (1 superfamily)
    trimer; one subunit consists of an alpha/beta oligomerization subdomain [3-stranded parallel beta-sheet, order 213], and an antiparallel coiled coil
  46. 2228704f.49: Proton glutamate symport protein [118214] (1 superfamily)
    multihelical membrane protein; partial structural duplication in the C-terminal region; oligomeric state: trimer
  47. 2228727f.50: Connexin43 [118219] (1 superfamily)
    mostly unstructured; 2 helices, hairpin
  48. 2228733f.51: Rhomboid-like [144090] (1 superfamily)
    6 transmembrane helices
  49. 2228773f.52: ATP synthase B chain-like [161059] (1 superfamily)
    long single helix, part of the stator subcomplex
  50. 2228780f.53: ATP synthase D chain-like [161064] (1 superfamily)
    non-globular, mostly helical component of the stator subcomplex
  51. 2228787f.54: SNF-like [161069] (1 superfamily)
    12 transmembrane helices; duplication: consists of two structurally similar halves
  52. 2228845f.55: Photosystem II antenna protein-like [161076] (1 superfamily)
    6 transmembrane helices arranged in three antiparallel pairs (hairpins), segregated by cofactors; there can be insertions of different small subdomains in different exposed loops
  53. 2228877f.56: MAPEG domain-like [161083] (1 superfamily)
    4 helices, bundle; left-handed superhelix
  54. 2228923f.57: MgtE membrane domain-like [161092] (1 superfamily)
    5 transmembrane helices; bundle, right-handed twist
  55. 2228934f.58: MetI-like [161097] (1 superfamily)
    core: 5 transmembrane helices; flattened bundle
  56. 2228983f.59: Cation efflux protein transmembrane domain-like [161110] (1 superfamily)
    6 transmembrane helices, bundle
  57. 2228996f.60: Anthrax protective antigen C-terminal-like [254103] (1 superfamily)
    C-terminal 3 domains; II (226-487) is beta-sandwiches of gamma-crystallin like topology, similar to domain I; III (488-594) has a beta-grasp like fold; IV (595-735) has an Ig-like fold
  58. 2229031f.61: Multidrug and toxic compound extrusion (MATE) transporter-like [310559] (1 superfamily)
  59. 2229042f.62: Diacylglycerol kinase (DgkA)-like [310569] (1 superfamily)
    forms homotrimer; each monomer has 3 transmembrane helices and one amphiphilic helix

More info for Class f: Membrane and cell surface proteins and peptides

Timeline for Class f: Membrane and cell surface proteins and peptides: