Class: All beta proteins

Lineage:

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

Folds:

1. Immunoglobulin-like beta-sandwich (20)
   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 (8)
   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 strands in 2 sheets
5. Penicillin-binding protein 5, C-terminal domain (1)
   sandwich; 6 strands in 2 sheets
6. alpha-Amylase inhibitor tendamistat (1)
   sandwich; 6 strands in 2 sheets
7. C-terminal domain of octopus hemocyanin (1)
   six-stranded beta-sandwich, jelly-roll/greek-key topology
8. Cupredoxin-like (2)
   sandwich; 7 strands in 2 sheets, greek-key
   variations: some members have additional 1-2 strands
9. C2 domain-like (4)
   sandwich; 8 strands in 2 sheets; greek-key
10. TRAF domain-like (1)
    sandwich; 8 strands in 2 sheets; greek-key
11. Neurophysin II (1)
    sandwich; 8 strands in 2 sheets; meander
12. N-utilization substance G protein NusG, insert domain (1)
    sandwich; 8 strands in 2 sheets; meander
13. Viral coat and capsid proteins (1)
    sandwich; 8 strands in 2 sheets; jelly-roll
    variations: some members have additional 1-2 strands
14. gamma-Crystallin-like (1)
    sandwich; 8 strands in 2 sheets; greek-key
    duplication: has internal pseudo twofold symmetry
15. Lipase/lipooxygenase domain (PLAT/LH2 domain) (1)
    sandwich; 8 strands in 2 sheets; complex topology
    duplication: has weak internal pseudo twofold symmetry
16. Nucleoplasmin/PNGase F-like (3)
    sandwich; 8 strands in 2 sheets; jelly-roll
17. Calpain large subunit, middle domain (domain III) (1)
    sandwich; 8 strands in 2 sheets; jelly-roll
18. Olfactory marker protein (1)
    sandwich; 8 strands in 2 sheets; jelly-roll
19. HSP20-like chaperones (1)
    sandwich; 8 strands in 2 sheets; greek-key
20. Ecotin, trypsin inhibitor (1)
    sandwich; 8 strands in 2 sheets; complex topology with the crossing loops
21. PEBP-like (1)
    sandwich; 8 strands in 2 sheets; greek-key: partial topological similarity to immunoglobulin-like folds
22. Ganglioside M2 (gm2) activator (1)
    sandwich; 8 strands in 2 sheets; greek-key: partial topological similarity to immunoglobulin-like folds
23. Nicotinic receptor ligand binding domain-like (1)
    sandwich; 8 strands in 2 sheets; greek-key: partial topological similarity to immunoglobulin-like folds
24. Galactose-binding domain-like (1)
    sandwich; 9 strands in 2 sheets; jelly-roll
25. Viral protein domain (1)
    sandwich; 9 strands in 2 sheets; jelly-roll; form trimers
26. Fucose-binding lectin II (PA-IIL) (1)
    sandwich; 9 strands in 2 sheets; greek-key
27. F-MuLV receptor-binding domain (1)
    sandwich; 9 strands in 2 sheets; greek-key; contains a few helices in loop regions
28. Virus attachment protein (1)
    sandwich, 10 strands in 2 sheets; greek-key
29. TNF-like (1)
    sandwich, 10 strands in 2 sheets; jelly-roll
30. Spermadhesin, CUB domain (1)
    sandwich, 10 strands in 2 sheets; jelly-roll
31. Hyaluronate lyase-like, C-terminal domain (1)
    sandwich, 10 strands in 2 sheets; "folded meander"
32. Equinatoxin II (eqtII, tenebrosin C) (1)
    sandwich, 10 strands in 2 sheets;
33. Osmotin, thaumatin-like protein (1)
    sandwich; 11 strands in 2 sheets
34. SMAD/FHA domain (1)
    sandwich; 11 strands in 2 sheets; greek-key
35. Soluble secreted chemokine inhibitor, VCCI (1)
    sandwich; 11 strands in 2 sheets; greek-key
36. Paculovirus p35 (1)
    sandwich; 14 strands in 2 sheets; greek-key
37. Concanavalin A-like lectins/glucanases (1)
    sandwich; 12-14 strands in 2 sheets; complex topology
38. Supersandwich (3)
    sandwich; 18 strands in 2 sheets
39. Leukotriene A4 hydrolase N-terminal domain (1)
    duplication: two beta-sandwiches of similar topologies are fused together in a single three beta-sheet domain
40. EV matrix protein (1)
    consists of two beta-sandwich domains of similar topologies
41. Viral chemokine binding protein m3 (1)
42. gp9 (1)
    consists of two different beta-sandwich domains unrelated to other beta-sandwich folds
43. 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)
44. Obg-fold (1)
    this fold is formed by three glycine-rich regions inserted into a small 8-stranded beta-sandwich
    these regions form six left-handed collagen-like helices packed and H-bonded together
45. SH3-like barrel (12)
    barrel, partly opened; n*=4, S*=8; meander
    the last strand is interrupted by a turn of 3-10 helix
46. GroES-like (2)
    contains barrel, partly opened; n*=4, S*=8; meander
47. PDZ domain-like (1)
    contains barrel, partly opened; n*=4, S*=8; meander; capped by alpha-helix
48. N-terminal domains of the minor coat protein g3p (1)
    core: barrel, in some members open; n*=4, S*=8; meander
49. Sm-like fold (2)
    core: barrel, open; n*=4, S*=8; meander; SH3-like topology
50. Ribosomal protein L14 (1)
    barrel, closed; n=5, S=8, meander
51. OB-fold (9)
    barrel, closed or partly opened n=5, S=10 or S=8; greek-key
52. Photosynthetic reaction centre, H-chain, cytoplasmic domain (1)
    core: barrel, partly opened; n*=5, S*=8; meander
53. beta-Trefoil (6)
    barrel, closed; n=6, S=12; and a hairpin triplet; meander
    duplication: has internal pseudo threefold symmetry
54. Reductase/isomerase/elongation factor common domain (4)
    barrel, closed; n=6, S=10; greek-key
55. EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain (1)
    barrel, closed; n=6, S=10; greek-key
56. FMN-binding split barrel (1)
    barrel; n=6, S=10; greek-key
57. Phage tail proteins (1)
    core: barrel; n=6, S=10; greek-key; topologically similar to the FMN-binding split barrel
58. FMT C-terminal domain-like (1)
    barrel, open; n*=6, S*=10; greek-key
59. Trypsin-like serine proteases (1)
    barrel, closed; n=6, S=8; greek-key
    duplication: consists of two domains of the same fold
60. mu transposase, C-terminal domain (1)
    barrel; n=6, S=8, greek-key
61. Domain of alpha and beta subunits of F1 ATP synthase-like (2)
    barrel, closed; n=6, S=8; greek-key
62. Small protein B (SmpB) (1)
    barrel, closed; n=6, S=8, greek-key, partial similarity to the OB-fold
63. Acid proteases (1)
    barrel, closed; n=6, S=10, complex topology
64. ValRS/IleRS/LeuRS editing domain (1)
    core: barrel, closed; n=6, S=8; topology is similar to that of the acid proteases barrel
65. Urease metallochaperone UreE, N-terminal domain (1)
    barrel, closed; n=6, S=8; a crossover loop topology
66. Double psi beta-barrel (2)
    barrel, closed; n=6, S=10; complex topology with crossover (psi) loops
67. Ribosomal protein L25-like (1)
    barrel, closed; n=6, S=10; complex topology
68. Core binding factor beta, CBF (1)
    barrel, closed; n=6, S=10; meander; capped at both ends by alpha-helices
69. PH domain-like (1)
    barrel, partly opened; n*=6, S*=12; meander; capped by an alpha-helix
70. Transcription factor IIA (TFIIA), N-terminal domain (1)
    barrel, closed; n=6, S=12; mixed beta-sheet
71. Herpes virus serine proteinase, assemblin (1)
    core: barrel, closed; n=7, S=8; complex topology
72. PK beta-barrel domain-like (1)
    barrel, closed; n=7, S=10; complex topology
73. XRCC4, N-terminal domain (1)
    barrel, closed; n=7, S=10; order: 1234765; strands 1 and 5 are parallel to each other
74. FAS1 domain (1)
    core: barrel, closed; n=7, S=12; meander
75. Lipocalins (1)
    barrel, closed or opened; n=8, S=12; meander
76. Streptavidin-like (5)
    barrel, closed; n=8, S=10; meander
77. Cyclophilin (peptidylprolyl isomerase) (1)
    barrel, closed; n=8, S=10; complex topology
78. Oncogene products (1)
    barrel, closed; n=8, S=10; one overside connection
79. Sortase (1)
    barrel, closed; n=8, S=10; mixed sheet; two overside connections
80. Mannose 6-phosphate receptor domain (1)
    barrel, partly open; n*=8, S*=10; one psi loop
81. triple 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
82. 4-bladed beta-propeller (1)
    consists of four 4-stranded beta-sheet motifs; meander
83. 5-bladed beta-propeller (2)
    consists of five 4-stranded beta-sheet motifs; meander
84. 6-bladed beta-propeller (7)
    consists of six 4-stranded beta-sheet motifs; meander
85. 7-bladed beta-propeller (10)
    consists of seven 4-stranded beta-sheet motifs; meander
86. 8-bladed beta-propeller (3)
    consists of eight 4-stranded beta-sheet motifs; meander
    also found in some members of the WD40-repeat superfamily
87. alpha-Amylases, C-terminal beta-sheet domain (1)
    folded sheet; greek-key
88. WW domain-like (2)
    core: 3-stranded meander beta-sheet
89. Head domain of nucleotide exchange factor GrpE (1)
    small mixed beta-sheet, 4 "generalized" strands
90. Ribonuclease domain of colicin E3 (1)
    twisted meander beta-sheet of 6 strands
91. Carbonic anhydrase (1)
    single sheet; 10 strands
92. Bacteriochlorophyll A protein (1)
    single sheet; 16 strands; meander
93. open-sided beta-meander (2)
    single sheet formed by beta-hairpin repeats; exposed on both sides in the middle
94. beta-Prism I (3)
    consists of 3 4-stranded sheets; strands are parallel to the 3-fold axis
    duplication: has internal pseudo threefold symmetry
95. 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
96. beta-Roll (1)
    contains a parallel beta-helix that binds calcium ions between its turns
97. Single-stranded right-handed beta-helix (5)
    superhelix with each turn made by 3 strands with short links
    duplication: turns of the helix are structural repeats
98. Single-stranded left-handed beta-helix (2)
    superhelix with each turn made by 3 strands with short links
99. Double-stranded beta-helix (7)
    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
100. Triple-stranded beta-helix (1)
     (homo)trimer; each chain donates 3 beta-strands per turn of the helix
101. Triple beta-spiral (1)
     trimer formed by the interlocking beta-hairpin repeat units
102. beta-hairpin stack (1)
     Trp-rich beta-hairpin repeat units form helical structures of 3 units per turn
103. Barrel-sandwich hybrid (3)
     sandwich of half-barrel shaped beta-sheets
104. beta-clip (7)
     double-stranded ribbon sharply bent in two places; the ribbon ends form incomplete barrel; jelly-roll
105. C-terminal autoproteolytic domain of nucleoporin nup98 (1)
     multisheet protein with a mixture of beta-sandwich and beta-prism features
106. Hedgehog/intein (Hint) domain (1)
     complex fold made of five beta-hairpin units and a b-ribbon arc
107. LexA/Signal peptidase (1)
     complex fold made of several coiled beta-sheets; contains an SH3-like barrel
108. Colicin E3 translocation domain (1)
     complex fold made of several coiled beta-sheets
109. Mss4-like (1)
     complex fold made of several coiled beta-sheets
110. Cyanovirin-N (1)
     complex fold
111. Tp47 lipoprotein, N-terminal domain (1)
     complex fold; consists of two intertwined subdomains
112. Methuselah ectodomain (1)
     complex fold
113. Head-binding domain of phage P22 tailspike protein (1)
     complex fold made of bifurcated and partly folded beta-sheet
114. E2 regulatory, transactivation domain (1)
     complex fold made of bifurcated and coiled beta-sheets
115. Molybdenum cofactor biosynthesis protein MoeA, N-terminal and linker domains (1)
     complex fold made of bifurcated and coiled b-sheets
116. Composite domain of metallo-dependent hydrolases (1)
     pseudobarrel; mixed sheet of 7 strand folded upon itself and "buckled" by two beta-turns
117. 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
118. N-terminal domain of MutM-like DNA repair proteins (1)
     pseudobarrel; capped on both ends by alpha-helices
119. P-domain of calnexin/calreticulin (1)
     non-globular proline-rich hairpin