SCOPe 2.06: Family d.58.7.1: Canonical RBD

Lineage for Family d.58.7.1: Canonical RBD

1. Root: SCOPe 2.06

2. Class d: Alpha and beta proteins (a+b) [53931] (385 folds)

3. Fold d.58: Ferredoxin-like [54861] (59 superfamilies)
   alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2

4. Superfamily d.58.7: RNA-binding domain, RBD [54928] (6 families)

5. Family d.58.7.1: Canonical RBD [54929] (68 proteins)

Proteins:

1. Alkylation repair AlkB homolog 8, ALKBH8 [143334] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [143335] (1 PDB entry)
     Uniprot Q96BT7 25-125

2. APOBEC1 stimulating protein [143326] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [143327] (1 PDB entry)
     Uniprot Q9NQ94 223-308

3. Arginine/serine-rich splicing factor 10 [143312] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [143313] (1 PDB entry)
     Uniprot P62995 109-191

4. Ataxin-2-binding protein 1 [143292] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [143293] (1 PDB entry)
     Uniprot Q9NWB1 109-196

5. Calcipressin-1 [117953] (1 species)

   • Species Mouse (Mus musculus) [TaxId:10090] [117954] (1 PDB entry)
     Uniprot Q9JHG6 14-103

6. CBP20, 20KDa nuclear cap-binding protein [64274] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [64275] (7 PDB entries)

7. Cleavage stimulation factor, 64 kda subunit [102983] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [102984] (1 PDB entry)

8. Cold-inducible RNA-binding protein [143300] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [143301] (1 PDB entry)
     Uniprot Q14011 1-90

9. CUG triplet repeat RNA-binding protein 1 [143336] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [143337] (2 PDB entries)
     Uniprot Q92879 383-484

10. E3 ubiquitin protein ligase CNOT4 [143294] (1 species)
    CCR4-NOT transcription complex subunit 4

    • Species Mouse (Mus musculus) [TaxId:10090] [143295] (1 PDB entry)
      Uniprot Q8BT14 101-198

11. Eukaryotic translation initiation factor 3 subunit 4 [143304] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [143305] (1 PDB entry)
      Uniprot O75821 231-320

12. Eukaryotic translation initiation factor 4B [117973] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [117974] (1 PDB entry)
      Uniprot P23588 88-178

13. Heterogeneous nuclear ribonucleoprotein d0 [54944] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [54945] (2 PDB entries)

14. Heterogeneous nuclear ribonucleoprotein H' [117955] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [117956] (2 PDB entries)
      Uniprot P55795 103-193; 280-369

15. Heterogeneous nuclear ribonucleoprotein L-like [117951] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [117952] (1 PDB entry)
      Uniprot Q921F4 116-207

16. Heterogeneous nuclear ribonucleoproteins A2/B1 [143342] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [143343] (1 PDB entry)
      Uniprot P22626 1-103

17. Heterogeneous nuclear ribonucleoproteins C1/C2 [117961] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [117962] (1 PDB entry)
      Uniprot P07910 8-92

18. HIV Tat-specific factor 1 [143290] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [143291] (1 PDB entry)
      Uniprot O43719 256-354

19. Hu antigen C (Huc) [54940] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [54941] (3 PDB entries)

20. Hu antigen D (Hud) [54942] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [54943] (2 PDB entries)

21. Hypothetical protein FLJ20273 [143328] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [143329] (1 PDB entry)
      Uniprot Q8NI52 150-245

22. IGF-II mRNA-binding protein 2 isoform A [143344] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [143345] (1 PDB entry)
      Uniprot Q9Y6M1 2-81

23. Limkain-b1, LKAP [143324] (1 species)
    KIAA0430

    • Species Human (Homo sapiens) [TaxId:9606] [143325] (1 PDB entry)
      Uniprot Q9Y4F3 788-870

24. Lupus LA protein [89940] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [89941] (8 PDB entries)

25. Matrin 3 [143306] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [143307] (2 PDB entries)
      Uniprot Q8K310 390-478! Uniprot Q8K310 478-576

26. Musashi-1 [102981] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [102982] (1 PDB entry)

27. Negative elongation factor E, NELF-E [143302] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [143303] (3 PDB entries)
      Uniprot P18615 257-335! Uniprot P18615 258-341

28. Neural RNA-binding protein Musashi-1 [54946] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [54947] (2 PDB entries)

29. Non-POU domain-containing octamer-binding protein, NonO [143354] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [143355] (2 PDB entries)
      Uniprot Q99K48 68-153

30. Nuclear factor Aly [102979] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [102980] (1 PDB entry)

31. Nuclear ribonucleoprotein A1 (RNP A1, UP1) [54930] (1 species)
    duplication: contains two domains of this fold

    • Species Human (Homo sapiens) [TaxId:9606] [54931] (14 PDB entries)
      Uniprot P09651 7-188

32. Nuclear ribonucleoprotein D0 (AUF1) [75439] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [75440] (1 PDB entry)

33. Nucleolin [54952] (2 species)

    1. Species Golden hamster (Mesocricetus auratus) [TaxId:10036] [54953] (4 PDB entries)

    2. Species Human (Homo sapiens) [TaxId:9606] [255371] (1 PDB entry)

34. Nucleolysin TIAR [143298] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [143299] (3 PDB entries)
      Uniprot Q01085 1-90! Uniprot Q01085 187-282

35. Nucleoporin 35 [143330] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [143331] (1 PDB entry)
      Uniprot Q8R4R6 169-249

36. Peptidyl-prolyl cis-trans isomerase E, N-terminal domain [143310] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [143311] (1 PDB entry)
      Uniprot Q9UNP9 1-89

37. Poly(A)-binding protein [54948] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [54949] (1 PDB entry)

38. Poly(A)-specific ribonuclease PARN [117967] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [117968] (1 PDB entry)
      Uniprot Q8VDG3 430-516; structure of the R3H domain (162-248) is also known (111031)

39. Polypyrimidine tract-binding protein [54950] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [54951] (7 PDB entries)
      Uniprot P26599 54-141, 177-284, 335-531

40. Polypyrimidine tract-binding protein 2, PTBP2 [143332] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [143333] (1 PDB entry)
      Uniprot Q9UKA9 51-138

41. Pre-mRNA branch site protein p14 [143316] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [143317] (2 PDB entries)
      Uniprot Q9Y3B4 12-125

42. Probable RNA-binding protein 19, Rbm19 [117969] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [117970] (4 PDB entries)
      Uniprot Q8R3C6 399-484; 581-678

43. Probable RNA-binding protein KIAA1579 [117963] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [117964] (1 PDB entry)
      Uniprot Q9HCJ3 71-145

44. Putative RNA-binding protein 15B, Rbm15b [117971] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [117972] (1 PDB entry)
      Uniprot Q6PHZ5 81-164

45. Ribonucleoprotein PTB-binding 1, Raver-1 [143308] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [143309] (1 PDB entry)
      Uniprot Q9CW46 61-135

46. RNA binding protein 23 [143352] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [143353] (2 PDB entries)
      Uniprot Q86U06 148-248

47. RNA-binding motif, single-stranded-interacting protein 1, RBMS1 [143356] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [143357] (1 PDB entry)
      Uniprot P29558 123-223

48. RNA-binding motif, single-stranded-interacting protein 2, RBMS2 [143320] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [143321] (1 PDB entry)
      Uniprot Q15434 58-129

49. RNA-binding protein 12 [143349] (2 species)
    3rd RBD

    1. Species Human (Homo sapiens) [TaxId:9606] [143350] (3 PDB entries)
       Uniprot Q9NTZ6 412-523! Uniprot Q9NTZ6 536-638

    2. Species Mouse (Mus musculus) [TaxId:10090] [143351] (1 PDB entry)
       Uniprot Q8R4X3 917-1002

50. RNA-binding protein 28 [143358] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [143359] (1 PDB entry)
      Uniprot Q8CGC6 316-413

51. RNA-binding protein 41, RBM41 [143296] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [143297] (1 PDB entry)
      Uniprot Q96IZ5 291-392

52. RNA-binding protein 8 [89938] (2 species)

    1. Species Fruit fly (Drosophila melanogaster) [TaxId:7227] [89939] (3 PDB entries)
       CG8781 protein

    2. Species Human (Homo sapiens) [TaxId:9606] [102978] (3 PDB entries)
       RBM8A, Y14

53. RNA-binding protein 9 [143314] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [143315] (1 PDB entry)
      Uniprot O43251 110-202

54. RNA-binding protein EWS [143340] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [143341] (1 PDB entry)
      Uniprot Q01844 353-453

55. RNA-binding protein Raly (Autoantigen p542) [117959] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [117960] (1 PDB entry)
      Uniprot Q9UKM9 1-97

56. RNA-binding protein UBP1 [143322] (1 species)

    • Species Trypanosoma cruzi [TaxId:5693] [143323] (1 PDB entry)
      Uniprot Q967R0 1-139

57. RNA-binding region containing protein 1 [143360] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [143361] (1 PDB entry)
      Uniprot Q9H0Z9 1-103

58. Sex-lethal protein [54938] (1 species)

    • Species Fruit fly (Drosophila melanogaster) [TaxId:7227] [54939] (4 PDB entries)

59. Splicesomal U1A protein [54932] (2 species)
    duplication: contains two domains of this fold

    1. Species Fruit fly (Drosophila melanogaster) [TaxId:7227] [160313] (3 PDB entries)
       Uniprot P43332 1-104! Uniprot P43332 134-216

    2. Species Human (Homo sapiens) [TaxId:9606] [54933] (50 PDB entries)
       Uniprot P09012 1-97 ! Uniprot P09012 4-98 ! Uniprot P09012 1-98

60. Splicing factor 3B subunit 4 [143318] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [143319] (2 PDB entries)
      Uniprot Q15427 102-184! Uniprot Q15427 4-96

61. Splicing factor U2AF 65 KDa subunit [54936] (2 species)

    1. Species Human (Homo sapiens) [TaxId:9606] [54937] (8 PDB entries)

    2. Species Mouse (Mus musculus) [TaxId:10090] [256391] (2 PDB entries)

62. Splicing factor U2B'' [54934] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [54935] (1 PDB entry)

63. Splicing factor, arginine/serine-rich 1, SFRS1 [143346] (2 species)

    1. Species Human (Homo sapiens) [TaxId:9606] [143347] (3 PDB entries)
       Uniprot Q07955 1-95

    2. Species Mouse (Mus musculus) [TaxId:10090] [143348] (1 PDB entry)
       Uniprot Q6PDM2 112-206

64. Splicing factor, arginine/serine-rich 9 (SFRS9) [117965] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [117966] (1 PDB entry)
      Uniprot Q9D0B0 104-188

65. Synaptojanin 2 [102985] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [102986] (1 PDB entry)

66. TAR DNA-binding protein 43, TDP-43 [117957] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [117958] (2 PDB entries)
      Uniprot Q13148 193-267

67. U4/U6 snRNA-associated-splicing factor PRP24 [143338] (1 species)
    contains three RBDs

    • Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [143339] (2 PDB entries)
      Uniprot P49960 116-196! Uniprot P49960 206-291! Uniprot P49960 41-115

68. automated matches [190332] (5 species)
    not a true protein

    1. Species Fruit fly (Drosophila melanogaster) [TaxId:7227] [311207] (1 PDB entry)

    2. Species Human (Homo sapiens) [TaxId:9606] [187155] (30 PDB entries)

    3. Species Mouse (Mus musculus) [TaxId:10090] [188825] (3 PDB entries)

    4. Species Nematode (Caenorhabditis elegans) [TaxId:6239] [258944] (3 PDB entries)

    5. Species Norway rat (Rattus norvegicus) [TaxId:10116] [272203] (1 PDB entry)

More info for Family d.58.7.1: Canonical RBD

Timeline for Family d.58.7.1: Canonical RBD:

• Family d.58.7.1: Canonical RBD first appeared (with stable ids) in SCOP 1.55
  
• Family d.58.7.1: Canonical RBD appears in SCOPe 2.05
  
• Family d.58.7.1: Canonical RBD appears in SCOPe 2.07
  
• Family d.58.7.1: Canonical RBD appears in the current release, SCOPe 2.08