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

  1. Root: SCOPe 2.08
  2. Class f: Membrane and cell surface proteins and peptides [56835] (69 folds)

Folds:

  1. f.1: Toxins' membrane translocation domains [56836] (5 superfamilies)
    multi-helical domains of various folds which is thought to unfold in the membrane
  2. f.3: Light-harvesting complex subunits [56917] (1 superfamily)
    membrane all-alpha fold
  3. f.4: Transmembrane beta-barrels [56924] (7 superfamilies)
    not a true fold, gathers together transmembrane barrels of different (n,S)
    annotated by the SCOP(e) curators as 'not a true fold'
  4. f.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. f.6: Leukocidin-like [56958] (1 superfamily)
    subunit fold contains beta-sandwich of Ig-like (greek-key) topology and a beta-ribbon arm that forms an oligomeric transmembrane barrel
  6. f.7: Lipovitellin-phosvitin complex; beta-sheet shell regions [56967] (1 superfamily)
    contains several large open beta-sheets
  7. f.8: Aerolisin/ETX pore-forming domain [56972] (1 superfamily)
    3 domains: (1) alpha+beta; (2&3) all-beta
  8. f.10: Viral glycoprotein, central and dimerisation domains [56982] (1 superfamily)
    2 intertwined domains; all-beta and alpha+beta
  9. f.12: Head and neck region of the ectodomain of NDV fusion glycoprotein [69921] (1 superfamily)
    3 intertwined all-beta domains
  10. f.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
  11. f.14: Gated ion channels [81325] (2 superfamilies)
    oligomeric transmembrane alpha-helical proteins
  12. f.15: Small-conductance potassium channel [81328] (1 superfamily)
    oligomeric transmembrane alpha-helical protein
  13. f.16: Gated mechanosensitive channel [81331] (1 superfamily)
    oligomeric transmembrane alpha-helical protein
  14. f.17: Transmembrane helix hairpin [81334] (6 superfamilies)
    two antiparallel transmembrane helices
  15. f.18: F1F0 ATP synthase subunit A [81337] (1 superfamily)
    core: up-and-down bundle of four transmembrane helices
  16. f.19: Aquaporin-like [81339] (1 superfamily)
    core: 8 helices, 2 short helices are surrounded by 6 long transmembrane helices
  17. f.20: Clc chloride channel [81341] (1 superfamily)
    core: 18 transmembrane helices
  18. f.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
  19. f.22: ABC transporter involved in vitamin B12 uptake, BtuC [81346] (1 superfamily)
    multihelical; complex architecture with several transmembrane helices
  20. f.23: Single transmembrane helix [81407] (42 superfamilies)
    not a true fold
    annotated by the SCOP(e) curators as 'not a true fold'
  21. f.24: Cytochrome c oxidase subunit I-like [81443] (1 superfamily)
    12 transmembrane helices in an approximate threefold rotational symmetric arrangement
  22. f.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
  23. f.26: Bacterial photosystem II reaction centre, L and M subunits [81484] (1 superfamily)
    five transmembrane helices forming a sheet-like structure
  24. f.27: 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81525] (1 superfamily)
    membrane-associated alpha-helical protein; no transmembrane helices
  25. f.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
  26. f.29: Photosystem I subunits PsaA/PsaB [81559] (1 superfamily)
    core:11 transmembrane helices
  27. f.30: Photosystem I reaction center subunit X, PsaK [81564] (1 superfamily)
    core: hairpin of two transmembrane helices
  28. f.31: Photosystem I reaction center subunit XI, PsaL [81569] (1 superfamily)
    core: three transmembrane helices, bundle
  29. f.32: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81649] (1 superfamily)
    core: three transmembrane helices, up-and-down bundle
  30. f.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
  31. f.34: Mechanosensitive channel protein MscS (YggB), transmembrane region [82860] (1 superfamily)
    oligomeric fold; 3 transmembrane helices per subunit
  32. f.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
  33. f.36: Neurotransmitter-gated ion-channel transmembrane pore [90111] (1 superfamily)
    heteropentameric transmembrane alpha-helical protein; 4 transmembrane helices per subunit
  34. f.37: ABC transporter transmembrane region [90122] (1 superfamily)
    multihelical; complex architecture with several transmembrane helices
  35. f.38: MFS general substrate transporter [103472] (1 superfamily)
    12 transmembrane helices; duplication: the N- and C-terminal halves are structurally similar
  36. f.40: V-type ATP synthase subunit C [103485] (1 superfamily)
    9 transmembrane helices
  37. f.41: Preprotein translocase SecY subunit [103490] (1 superfamily)
    10 transmembrane helices forming of a gated channel
  38. f.42: Mitochondrial carrier [103505] (1 superfamily)
    membrane all-alpha fold; 6-helical "barrel" with internal binding cavity
  39. f.43: Chlorophyll a-b binding protein [103510] (1 superfamily)
    membrane all-alpha fold; three transmembrane helices
  40. f.44: Ammonium transporter [111351] (1 superfamily)
    11 transmembrane helices; duplication: consist of 2 structural repeats of five helices each plus extra C-terminal helix
  41. f.45: Mitochondrial ATP synthase coupling factor 6 [111356] (1 superfamily)
    2 helices, hairpin
  42. f.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))
  43. f.47: VP4 membrane interaction domain [111378] (1 superfamily)
    2 domains; d1: complexed all-beta fold; d2: coiled-coil (trimeric) helical region
  44. f.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
  45. f.49: Proton glutamate symport protein [118214] (1 superfamily)
    multihelical membrane protein; partial structural duplication in the C-terminal region; oligomeric state: trimer
  46. f.50: Connexin43 [118219] (1 superfamily)
    mostly unstructured; 2 helices, hairpin
  47. f.51: Rhomboid-like [144090] (1 superfamily)
    6 transmembrane helices
  48. f.52: ATP synthase B chain-like [161059] (1 superfamily)
    long single helix, part of the stator subcomplex
  49. f.53: ATP synthase D chain-like [161064] (1 superfamily)
    non-globular, mostly helical component of the stator subcomplex
  50. f.54: SNF-like [161069] (1 superfamily)
    12 transmembrane helices; duplication: consists of two structurally similar halves
  51. f.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
  52. f.56: MAPEG domain-like [161083] (1 superfamily)
    4 helices, bundle; left-handed superhelix
  53. f.57: MgtE membrane domain-like [161092] (1 superfamily)
    5 transmembrane helices; bundle, right-handed twist
  54. f.58: MetI-like [161097] (1 superfamily)
    core: 5 transmembrane helices; flattened bundle
  55. f.59: Cation efflux protein transmembrane domain-like [161110] (1 superfamily)
    6 transmembrane helices, bundle
  56. f.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
  57. f.61: Multidrug and toxic compound extrusion (MATE) transporter-like [310559] (1 superfamily)
    12 transmembrane helices, in two bundles of 6
  58. f.62: Diacylglycerol kinase (DgkA)-like [310569] (1 superfamily)
    forms homotrimer; each monomer has 3 transmembrane helices and one amphiphilic helix
  59. f.63: Claudin-like [345895] (1 superfamily)
    4 transmembrane helices with 5-strand antiparallel beta-sheet, order 43215, on one side of membrane
  60. f.64: Filovirus surface glycoprotein-like [418716] (1 superfamily)
    pre-fusion conformation with complex fold including several alpha+beta domains
  61. f.65: Vacuolar ATP synthase subunit a (also called I subunit) C-terminal domain [418717] (1 superfamily)
    eight long membrane-embedded helices
  62. f.66: Helical insert domain of RAG1 [418718] (1 superfamily)
    bundle of 6 to 8 helices, somewhat irregular
  63. f.67: Bestropin channel-like [418719] (1 superfamily)
    four transmembrane helices; forms pentameric pore channel
  64. f.68: Anoctamin (TMEM16)-like [418720] (2 superfamilies)
    10 or 11 transmembrane helices, forms dimers
  65. f.69: Perfringolysin N-terminal-like [418706] (1 superfamily)
    twisted 4-strand antiparallel beta sheet, surrounded by other helices and strands, complex topology
  66. f.70: Extracellular adhesion domain of SabA-like [418729] (1 superfamily)
    club-like mostly helical structure; central region has similarity to 4-helix bundles such as bromodomains (a.29.6)
  67. f.71: LYR proteins from mammalian respiratory complex I [418731] (1 superfamily)
    three-helix bundle, with long extended loops that interact with other subunits
  68. f.72: Antiporter-like subunits from respiratory complex I [418732] (1 superfamily)
    core: 14 transmembrane helices; each has two groups of five helices are related to each other by pseudo two-fold symmetry, with the groups inverted with respect to the membrane
  69. f.73: Non-antiporter membrane subunits from respiratory complex I [418733] (3 superfamilies)
    Three subunits form a single 11-helix bundle at the interface between the hydrophilic domain and the antiporter-like subunits

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

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