Class: All beta proteins

Lineage:

1. Root: scop
2. Class: All beta proteins

Folds:

1. Immunoglobulin-like beta-sandwich (14)
   sandwich; 7 strands in 2 sheets; greek-key
   some members of the fold have additional strands
2. Common fold of diphtheria toxin/transcription factors/cytochrome f (7)
   sandwich; 9 strands in 2 sheet; greek-key; subclass of immunoglobin-like fold
3. Prealbumin-like (6)
   sandwich; 7 strands in 2 sheets, greek-key
   variations: some members have additional 1-2 strands to common fold
4. HSP40/DnaJ peptide-binding domain (1)
   sandwich; 6-6 strands in 2 sheets
5. alpha-Amylase inhibitor tendamistat (1)
   sandwich; 6 strands in 2 sheets
6. Cupredoxins (1)
   sandwich; 7 strands in 2 sheets, greek-key
   variations: some memmbers have additional 1-2 strands
7. C2 domain-like (4)
   sandwich; 8 strands in 2 sheets; greek-key
8. TRAF domain (1)
   sandwich; 8 strands in 2 sheets; greek-key
9. Neurophysin II (1)
   sandwich; 8 strands in 2 sheets; meander
10. Viral coat and capsid proteins (1)
    sandwich; 8 strands in 2 sheets; jelly-roll
    variations: some members have additional 1-2 strands
11. gamma-Crystallin-like (1)
    sandwich; 8 strands in 2 sheets; greek-key
    duplication: has internal pseudo twofold symmetry
12. Lipase/lipooxygenase domain (1)
    sandwich; 8 strands in 2 sheets; complex topology
    duplication: has weak internal pseudo twofold symmetry
13. PNGase F-like (2)
    sandwich; 8 strands in 2 sheets; jelly-roll; duplication: consists of two domains of this fold that pack together in a similar assymetric fasion
14. Calpain large subunit, middle domain (domain III) (1)
    sandwich; 8 strands in 2 sheets; jelly-roll
15. HSP20-like chaperones (1)
    sandwich; 8 strands in 2 sheets; greek-key
16. Ecotin, trypsin inhibitor (1)
    sandwich; 8 strands in 2 sheets; complex topology with the crossing loops
17. Phosphatidylethanolamine binding protein (1)
    sandwich; 8 strands in 2 sheets; greek-key: partial topological similarity to immunoglobulin-like folds
18. Galactose-binding domain-like (1)
    sandwich; 9 strands in 2 sheets; jelly-roll
19. Segmented RNA-genome viruses' proteins (1)
    sandwich; 9 strands in 2 sheets; jelly-roll; form trimers
20. F-MuLV receptor-binding domain (1)
    sandwich; 9 strands in 2 sheets; greek-key; contains a few helices in loop regions
21. Adenovirus fiber protein head domain (knob domain) (1)
    sandwich, 10 strands in 2 sheets; greek-key
22. TNF-like (1)
    sandwich, 10 strands in 2 sheets; jelly-roll
23. Spermadhesin, CUB domain (1)
    sandwich, 10 strands in 2 sheets; jelly-roll
24. Hyaluronate lyase-like, C-terminal domain (1)
    sandwich, 10 strands in 2 sheets; "folded meander"
25. Osmotin, thaumatin-like protein (1)
    sandwich; 11 strands in 2 sheets
26. SMAD/FHA domain (1)
    sandwich; 11 strands in 2 sheets; greek-key
27. Soluble secreted chemokine inhibitor, VCCI (1)
    sandwich; 11 strands in 2 sheets; greek-key
28. Paculovirus p35 (1)
    sandwich; 14 strands in 2 sheets; greek-key
29. Concanavalin A-like lectins/glucanases (1)
    sandwich; 12-14 strands in 2 sheets; complex topology
30. Supersandwich (3)
    sandwich; 18 strands in 2 sheets
31. EV matrix protein (1)
    consists of two beta-sandwich domains of similar topologies
32. gp9 (1)
    consists of two different beta-sandwich domains unrelated to other beta-sandwich folds
33. ISP domain (1)
    consists of two all-beta subdomains: conserved small domain has a rubredoxin-like fold; larger domain consists of 6 beta-stands packed in either sandwich of two 3-stranded sheets or closed barrel (n=6; S=8)
34. SH3-like barrel (7)
    barrel, partly opened; n*=4, S*=8; meander
    the last strand is interrupted by a turn of 3-10 helix
35. GroES-like (2)
    contains barrel, partly opened; n*=4, S*=8; meander
36. PDZ domain-like (1)
    contains barrel, partly opened; n*=4, S*=8; meander; capped by alpha-helix
37. N-terminal domains of the minor coat protein g3p (1)
    core: barrel, in some members open; n*=4, S*=8; meander
38. Sm motif of small nuclear ribonucleoproteins, SNRNP (1)
    core: barrel, open; n*=4, S*=8; meander; SH3-like topology
39. Ribosomal protein L14 (1)
    barrel, closed; n=5, S=8, meander
40. OB-fold (7)
    barrel, closed or partly opened n=5, S=10 or S=8; greek-key
41. Photosynthetic reaction centre, H-chain, cytoplasmic domain (1)
    core: barrel, partly opened; n*=5, S*=8; meander
42. beta-Trefoil (5)
    barrel, closed; n=6, S=12; and a hairpin triplet; meander
    duplication: has internal pseudo threefold symmetry
43. Reductase/isomerase/elongation factor common domain (3)
    barrel, closed; n=6, S=10; greek-key
44. EF-Tu/eEF-1alpha C-terminal domain (1)
    barrel, closed; n=6, S=10; greek-key
45. FMN-binding split barrel (1)
    barrel; n=6, S=10; greek-key
46. FMT C-terminal domain-like (1)
    barrel, open; n*=6, S*=10; greek-key
47. Trypsin-like serine proteases (1)
    barrel, closed; n=6, S=8; greek-key
    duplication: consists of two domains of the same fold
48. mu transposase, C-terminal domain (1)
    barrel; n=6, S=8, greek-key
49. Domain of alpha and beta subunits of F1 ATP synthase-like (2)
    barrel, closed; n=6, S=8; greek-key
50. Acid proteases (1)
    barrel, closed; n=6, S=10, complex topology
51. ValRS/IleRS editing domain (1)
    core: barrel, closed; n=6, S=8; topology is similar to that of the acid proteases barrel
52. Double psi beta-barrel (2)
    barrel, closed; n=6, S=10; complex topology with crossover (psi) loops
53. Ribosomal protein L25-like (1)
    barrel, closed; n=6, S=10; complex topology
54. Core binding factor beta (1)
    barrel, closed; n=6, S=10; meander; capped at both ends by alpha-helices
55. PH domain-like (1)
    barrel, partly opened; n*=6, S*=12; meander; capped by an alpha-helix
56. Transcription factor IIA (TFIIA), N-terminal domain (1)
    barrel, closed; n=6, S=12; mixed beta-sheet
57. Herpes virus serine proteinase, assemblin (1)
    core: barrel, closed; n=7, S=8; complex topology
58. Pyruvate kinase beta-barrel domain (1)
    barrel, closed; n=7, S=10; complex topology
59. XRCC4, N-terminal domain (1)
    barrel, closed; n=7, S=10; order: 1234765; strands 1 and 5 are parallel to each other
60. Lipocalins (1)
    barrel, closed or opened; n=8, S=12; meander
61. Streptavidin-like (3)
    barrel, closed; n=8, S=10; meander
62. Cyclophilin (peptidylprolyl isomerase) (1)
    barrel, closed; n=8, S=10; complex topology
63. Oncogene products (1)
    barrel, closed; n=8, S=10; one overside connection
64. Extracytoplasmic domain of cation-dependent mannose 6-phosphate receptor (1)
    barrel, partly open; n*=8, S*=10; one psi loop
65. tripple barrel (1)
    dimer of two non-identical subunits; forms two similar barrels, n=8, S=10 each, that are fused together with the formation of third barrel, n=6, S=8
66. 4-bladed beta-propeller (1)
    consists of four 4-stranded beta-sheet motifs; meander
67. 5-bladed beta-propeller (1)
    consists of five 4-stranded beta-sheet motifs; meander
68. 6-bladed beta-propeller (4)
    consists of six 4-stranded beta-sheet motifs; meander
69. 7-bladed beta-propeller (7)
    consists of seven 4-stranded beta-sheet motifs; meander
70. 8-bladed beta-propeller (2)
    consists of eight 4-stranded beta-sheet motifs; meander
71. alpha-Amylases, C-terminal beta-sheet domain (1)
    folded sheet; greek-key
72. WW domain-like (2)
    core: 3-stranded meander beta-sheet
73. Head domain of nucleotide exchange factor GrpE (1)
    small mixed beta-sheet, 4 "generalized" strands
74. Carbonic anhydrase (1)
    single sheet; 10 strands
75. Bacteriochlorophyl A protein (1)
    single sheet; 16 strands; meander
76. Outer surface protein A (1)
    single sheet; 21 strands; meander; the middle part is exposed on both sides
    duplication: contains beta-hairpin repeats
77. beta-Prism I (3)
    consists of 3 4-stranded sheets; strands are parallel to the 3-fold axis
    duplication: has internal pseudo threefold symmetry
78. beta-Prism II (1)
    consists of 3 4-stranded sheets; strands are perpendicular to the 3-fold axis
    duplication: consists of two domains of this fold
79. beta-Roll (1)
    contains a parallel beta-helix that binds calcium ions between its turns
80. Single-stranded right-handed beta-helix (2)
    superhelix with each turn made by 3 strands with short links
    duplication: turns of the helix are structural repeats
81. Single-stranded left-handed beta-helix (2)
    superhelix with each turn made by 3 strands with short links
82. Double-stranded beta-helix (5)
    one turn of helix is made by two pairs of antiparallel strands linked with short turns
    has appearance of a sandwich of distinct architecture and jelly-roll topology
83. Triple beta-spiral (1)
    trimer formed by the interlocking beta-hairpin repeat units
84. Barrel-sandwich hybrid (3)
    sandwich of half-barrel shaped beta-sheets
85. beta-clip (5)
    double-stranded ribbon sharply bent in two places; the ribbon ends form incomplete barrel; jelly-roll
86. Hedgehog/intein (Hint) domain (1)
    complex fold made of five beta-hairpin units and a b-ribbon arc
87. LexA/Signal peptidase (1)
    complex fold made of several coiled beta-sheets; contains an SH3-like barrel
88. RabGEF Mss4 (1)
    complex fold made of several coiled beta-sheets
89. Cyanovirin-N (1)
    complex fold made of two three stranded beta-sheets and two beta-hairpins
90. Head-binding domain of phage p22 tailspike protein (1)
    complex fold made of bifurcated and partly folded b-sheet
91. E2 regulatory, transactivation domain (1)
    complex fold made of bifurcated and coiled b-sheets
92. alpha-Subunit of urease, composite domain (1)
    pseudobarrel; mixed sheet of 7 strand folded upon itself and "buckled" by two beta-turns
93. Epsilon subunit of F1F0-ATP synthase N-terminal domain (1)
    pseudobarrel: sandwich of two sheets packed at a positive interstrand angle and interconnected with many short turns