Structural Classification of Proteins
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Superfamily: RNA-binding domain, RBD

link to SUPERFAMILY database - Superfamily

Lineage:

  1. Root: scop
  2. Class: Alpha and beta proteins (a+b) [53931]
    Mainly antiparallel beta sheets (segregated alpha and beta regions)
  3. Fold: Ferredoxin-like [54861]
    alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
  4. Superfamily: RNA-binding domain, RBD [54928]
    link to SUPERFAMILY database - Superfamily

Families:

  1. Canonical RBD [54929] (71)
    1. Nuclear ribonucleoprotein A1 (RNP A1, UP1) [54930]
      duplication: contains two domains of this fold
      1. Human (Homo sapiens) [TaxId: 9606] [54931] (14) picpic
        SQ P09651 7-188
    2. Nuclear ribonucleoprotein D0 (AUF1) [75439]
      1. Human (Homo sapiens) [TaxId: 9606] [75440] (3) picpic
    3. Splicesomal U1A protein [54932]
      duplication: contains two domains of this fold
      1. Human (Homo sapiens) [TaxId: 9606] [54933] (38) picpic
        SQ P09012 1-97 ! SQ P09012 4-98 ! SQ P09012 1-98
      2. Drosophila melanogaster [TaxId: 7227] [160313] (3) picpic
        SQ P43332 1-104! SQ P43332 134-216
    4. Splicing factor U2B'' [54934]
      1. Human (Homo sapiens) [TaxId: 9606] [54935] (1) picpic
    5. Splicing factor U2AF 65 KDa subunit [54936]
      1. Human (Homo sapiens) [TaxId: 9606] [54937] (4) picpic
    6. Sex-lethal protein [54938]
      1. Drosophila melanogaster [TaxId: 7227] [54939] (4) picpic
    7. Hu antigen C (Huc) [54940]
      1. Mouse (Mus musculus) [TaxId: 10090] [54941] (3) picpic
    8. Hu antigen D (Hud) [54942]
      1. Human (Homo sapiens) [TaxId: 9606] [54943] (2) picpic
    9. Heterogeneous nuclear ribonucleoprotein d0 [54944]
      1. Human (Homo sapiens) [TaxId: 9606] [54945] (2) picpic
    10. Neural RNA-binding protein Musashi-1 [54946]
      1. Mouse (Mus musculus) [TaxId: 10090] [54947] (2) picpic
    11. Poly(A)-binding protein [54948]
      1. Human (Homo sapiens) [TaxId: 9606] [54949] (1) picpic
    12. Polypyrimidine tract-binding protein [54950]
      1. Human (Homo sapiens) [TaxId: 9606] [54951] (9) picpic
        SQ P26599 54-141, 177-284, 335-531
    13. Nucleolin [54952]
      1. Golden hamster (Mesocricetus auratus) [TaxId: 10036] [54953] (4) picpic
    14. CBP20, 20KDa nuclear cap-binding protein [64274]
      1. Human (Homo sapiens) [TaxId: 9606] [64275] (6) picpic
    15. RNA-binding protein 8 [89938]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [89939] (3) picpic
        CG8781 protein
      2. Human (Homo sapiens) [TaxId: 9606] [102978] (6) picpic
        RBM8A, Y14
    16. Lupus LA protein [89940]
      1. Human (Homo sapiens) [TaxId: 9606] [89941] (13) picpic
    17. Nuclear factor Aly [102979]
      1. Mouse (Mus musculus) [TaxId: 10090] [102980] (1) picpic
    18. Musashi-1 [102981]
      1. Mouse (Mus musculus) [TaxId: 10090] [102982] (1) picpic
    19. Cleavage stimulation factor, 64 kda subunit [102983]
      1. Human (Homo sapiens) [TaxId: 9606] [102984] (1) picpic
    20. Synaptojanin 2 [102985]
      1. Human (Homo sapiens) [TaxId: 9606] [102986] (1) picpic
    21. Heterogeneous nuclear ribonucleoprotein L-like [117951]
      1. Mouse (Mus musculus) [TaxId: 10090] [117952] (1) picpic
        SQ Q921F4 116-207
    22. Calcipressin-1 [117953]
      1. Mouse (Mus musculus) [TaxId: 10090] [117954] (1) picpic
        SQ Q9JHG6 14-103
    23. Heterogeneous nuclear ribonucleoprotein H' [117955]
      1. Human (Homo sapiens) [TaxId: 9606] [117956] (2) picpic
        SQ P55795 103-193; 280-369
    24. TAR DNA-binding protein 43, TDP-43 [117957]
      1. Human (Homo sapiens) [TaxId: 9606] [117958] (2) picpic
        SQ Q13148 193-267
    25. RNA-binding protein Raly (Autoantigen p542) [117959]
      1. Human (Homo sapiens) [TaxId: 9606] [117960] (1) picpic
        SQ Q9UKM9 1-97
    26. Heterogeneous nuclear ribonucleoproteins C1/C2 [117961]
      1. Human (Homo sapiens) [TaxId: 9606] [117962] (1) picpic
        SQ P07910 8-92
    27. Probable RNA-binding protein KIAA1579 [117963]
      1. Human (Homo sapiens) [TaxId: 9606] [117964] (1) picpic
        SQ Q9HCJ3 71-145
    28. Splicing factor, arginine/serine-rich 9 (SFRS9) [117965]
      1. Mouse (Mus musculus) [TaxId: 10090] [117966] (1) picpic
        SQ Q9D0B0 104-188
    29. Poly(A)-specific ribonuclease PARN [117967]
      1. Mouse (Mus musculus) [TaxId: 10090] [117968] (1) picpic
        SQ Q8VDG3 430-516; structure of the R3H domain (162-248) is also known (scop_sp 111031)
    30. Probable RNA-binding protein 19, Rbm19 [117969]
      1. Mouse (Mus musculus) [TaxId: 10090] [117970] (4) picpic
        SQ Q8R3C6 399-484; 581-678
    31. Putative RNA-binding protein 15B, Rbm15b [117971]
      1. Mouse (Mus musculus) [TaxId: 10090] [117972] (1) picpic
        SQ Q6PHZ5 81-164
    32. Eukaryotic translation initiation factor 4B [117973]
      1. Human (Homo sapiens) [TaxId: 9606] [117974] (1) picpic
        SQ P23588 88-178
    33. HIV Tat-specific factor 1 [143290]
      1. Human (Homo sapiens) [TaxId: 9606] [143291] (1) picpic
        SQ O43719 256-354
    34. Ataxin-2-binding protein 1 [143292]
      1. Human (Homo sapiens) [TaxId: 9606] [143293] (1) picpic
        SQ Q9NWB1 109-196
    35. E3 ubiquitin protein ligase CNOT4 [143294]
      CCR4-NOT transcription complex subunit 4
      1. Mouse (Mus musculus) [TaxId: 10090] [143295] (1) picpic
        SQ Q8BT14 101-198
    36. RNA-binding protein 41, RBM41 [143296]
      1. Human (Homo sapiens) [TaxId: 9606] [143297] (1) picpic
        SQ Q96IZ5 291-392
    37. Nucleolysin TIAR [143298]
      1. Human (Homo sapiens) [TaxId: 9606] [143299] (2) picpic
        SQ Q01085 1-90! SQ Q01085 187-282
    38. Cold-inducible RNA-binding protein [143300]
      1. Human (Homo sapiens) [TaxId: 9606] [143301] (1) picpic
        SQ Q14011 1-90
    39. Negative elongation factor E, NELF-E [143302]
      1. Human (Homo sapiens) [TaxId: 9606] [143303] (3) picpic
        SQ P18615 257-335! SQ P18615 258-341
    40. Eukaryotic translation initiation factor 3 subunit 4 [143304]
      1. Human (Homo sapiens) [TaxId: 9606] [143305] (1) picpic
        SQ O75821 231-320
    41. Matrin 3 [143306]
      1. Mouse (Mus musculus) [TaxId: 10090] [143307] (2) picpic
        SQ Q8K310 390-478! SQ Q8K310 478-576
    42. Ribonucleoprotein PTB-binding 1, Raver-1 [143308]
      1. Mouse (Mus musculus) [TaxId: 10090] [143309] (1) picpic
        SQ Q9CW46 61-135
    43. Peptidyl-prolyl cis-trans isomerase E, N-terminal domain [143310]
      1. Human (Homo sapiens) [TaxId: 9606] [143311] (1) picpic
        SQ Q9UNP9 1-89
    44. Arginine/serine-rich splicing factor 10 [143312]
      1. Human (Homo sapiens) [TaxId: 9606] [143313] (1) picpic
        SQ P62995 109-191
    45. RNA-binding protein 9 [143314]
      1. Human (Homo sapiens) [TaxId: 9606] [143315] (1) picpic
        SQ O43251 110-202
    46. Pre-mRNA branch site protein p14 [143316]
      1. Human (Homo sapiens) [TaxId: 9606] [143317] (4) picpic
        SQ Q9Y3B4 12-125
    47. Splicing factor 3B subunit 4 [143318]
      1. Human (Homo sapiens) [TaxId: 9606] [143319] (2) picpic
        SQ Q15427 102-184! SQ Q15427 4-96
    48. RNA-binding motif, single-stranded-interacting protein 2, RBMS2 [143320]
      1. Human (Homo sapiens) [TaxId: 9606] [143321] (1) picpic
        SQ Q15434 58-129
    49. RNA-binding protein UBP1 [143322]
      1. Trypanosoma cruzi [TaxId: 5693] [143323] (1) picpic
        SQ Q967R0 1-139
    50. Limkain-b1, LKAP [143324]
      KIAA0430
      1. Human (Homo sapiens) [TaxId: 9606] [143325] (1) picpic
        SQ Q9Y4F3 788-870
    51. APOBEC1 stimulating protein [143326]
      1. Human (Homo sapiens) [TaxId: 9606] [143327] (1) picpic
        SQ Q9NQ94 223-308
    52. Hypothetical protein FLJ20273 [143328]
      1. Human (Homo sapiens) [TaxId: 9606] [143329] (1) picpic
        SQ Q8NI52 150-245
    53. Nucleoporin 35 [143330]
      1. Mouse (Mus musculus) [TaxId: 10090] [143331] (4) picpic
        SQ Q8R4R6 169-249
    54. Polypyrimidine tract-binding protein 2, PTBP2 [143332]
      1. Human (Homo sapiens) [TaxId: 9606] [143333] (1) picpic
        SQ Q9UKA9 51-138
    55. Alkylation repair AlkB homolog 8, ALKBH8 [143334]
      1. Human (Homo sapiens) [TaxId: 9606] [143335] (1) picpic
        SQ Q96BT7 25-125
    56. CUG triplet repeat RNA-binding protein 1 [143336]
      1. Human (Homo sapiens) [TaxId: 9606] [143337] (1) picpic
        SQ Q92879 383-484
    57. U4/U6 snRNA-associated-splicing factor PRP24 [143338]
      contains three RBDs
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [143339] (24) picpic
        SQ P49960 116-196! SQ P49960 206-291! SQ P49960 41-115
    58. RNA-binding protein EWS [143340]
      1. Human (Homo sapiens) [TaxId: 9606] [143341] (1) picpic
        SQ Q01844 353-453
    59. Heterogeneous nuclear ribonucleoproteins A2/B1 [143342]
      1. Human (Homo sapiens) [TaxId: 9606] [143343] (1) picpic
        SQ P22626 1-103
    60. IGF-II mRNA-binding protein 2 isoform A [143344]
      1. Human (Homo sapiens) [TaxId: 9606] [143345] (1) picpic
        SQ Q9Y6M1 2-81
    61. Splicing factor, arginine/serine-rich 1, SFRS1 [143346]
      1. Human (Homo sapiens) [TaxId: 9606] [143347] (3) picpic
        SQ Q07955 1-95
      2. Mouse (Mus musculus) [TaxId: 10090] [143348] (1) picpic
        SQ Q6PDM2 112-206
    62. RNA-binding protein 12 [143349]
      3rd RBD
      1. Human (Homo sapiens) [TaxId: 9606] [143350] (2) picpic
        SQ Q9NTZ6 412-523! SQ Q9NTZ6 536-638
      2. Mouse (Mus musculus) [TaxId: 10090] [143351] (1) picpic
        SQ Q8R4X3 917-1002
    63. RNA binding protein 23 [143352]
      1. Human (Homo sapiens) [TaxId: 9606] [143353] (1) picpic
        SQ Q86U06 148-248
    64. Non-POU domain-containing octamer-binding protein, NonO [143354]
      1. Mouse (Mus musculus) [TaxId: 10090] [143355] (1) picpic
        SQ Q99K48 68-153
    65. RNA-binding motif, single-stranded-interacting protein 1, RBMS1 [143356]
      1. Human (Homo sapiens) [TaxId: 9606] [143357] (1) picpic
        SQ P29558 123-223
    66. RNA-binding protein 28 [143358]
      1. Mouse (Mus musculus) [TaxId: 10090] [143359] (1) picpic
        SQ Q8CGC6 316-413
    67. RNA-binding region containing protein 1 [143360]
      1. Human (Homo sapiens) [TaxId: 9606] [143361] (1) picpic
        SQ Q9H0Z9 1-103
  2. Non-canonical RBD domain [54954] (1)
    1. mRNA export factor tap [54955]
      1. Human (Homo sapiens) [TaxId: 9606] [54956] (5) picpic
  3. Splicing factor U2AF subunits [64276] (1)
    1. U2AF35 (35 KDa subunit) [64277]
      1. Human (Homo sapiens) [TaxId: 9606] [64278] (1) picpic
  4. Smg-4/UPF3 [102987] (1)
    Pfam 03467
    1. RNA processing protein UPF3x, RRM domain [102988]
      1. Human (Homo sapiens) [TaxId: 9606] [102989] (1) picpic
  5. GUCT domain [160314] (1)
    Pfam 08152
    1. ATP-dependent RNA helicase DDX50 [160315]
      1. Human (Homo sapiens) [TaxId: 9606] [160316] (1) picpic
        SQ Q9BQ39 575-659
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MRC site Generated from scop database 1.75 with scopm 1.101 on Wed Jun 3 10:42:06 2009
Copyright © 1994-2009 The scop authors / scop@mrc-lmb.cam.ac.uk