SCOPe 2.04: Family d.15.1.1: Ubiquitin-related

Lineage for Family d.15.1.1: Ubiquitin-related

1. Root: SCOPe 2.04

2. Class d: Alpha and beta proteins (a+b) [53931] (380 folds)

3. Fold d.15: beta-Grasp (ubiquitin-like) [54235] (14 superfamilies)
   core: beta(2)-alpha-beta(2); mixed beta-sheet 2143

4. Superfamily d.15.1: Ubiquitin-like [54236] (9 families)

5. Family d.15.1.1: Ubiquitin-related [54237] (39 proteins)
   Pfam PF00240

Proteins:

1. 1700011n24rik protein [110796] (1 species)

   • Species Mouse (Mus musculus) [TaxId:10090] [110797] (1 PDB entry)
     Uniprot Q9DAF3 1-89

2. 2'-5'-oligoadenylate synthetase-like protein, OASL [117808] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [117809] (1 PDB entry)
     Uniprot Q15646 434-507

3. 4931431F19Rik [142950] (1 species)

   • Species Mouse (Mus musculus) [TaxId:10090] [142951] (1 PDB entry)
     Uniprot Q9D4I8 14-96
     structure of the C-terminal UBA domain is also known (PDB 1vej)

4. 8430435i17rik protein [110798] (1 species)

   • Species Mouse (Mus musculus) [TaxId:10090] [110799] (1 PDB entry)
     Uniprot Q8BGR9 3-79

5. Bag-family molecular chaperone regulator-1 [142932] (2 species)

   1. Species Human (Homo sapiens) [TaxId:9606] [142933] (1 PDB entry)
      Uniprot Q99933 72-152
      the BAG domain structure is also known (63494)

   2. Species Mouse (Mus musculus) [TaxId:10090] [255463] (2 PDB entries)

6. Dendritic cell-derived ubiquitin-like protein [142954] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [142955] (1 PDB entry)
     Uniprot Q8WUN7 149-228

7. DSK2 [142940] (1 species)

   • Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [142941] (1 PDB entry)
     Uniprot P48510 2-74

8. Elongin B [54246] (2 species)

   1. Species Human (Homo sapiens) [TaxId:9606] [54247] (16 PDB entries)

   2. Species Mouse (Mus musculus) [TaxId:10090] [142930] (1 PDB entry)
      Uniprot P62869 1-98

9. Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1 [117802] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [117803] (1 PDB entry)
     Uniprot Q15011 10-90

10. hypothetical D7wsu128e protein [110800] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [110801] (1 PDB entry)
      Uniprot Q78JW9 76-157

11. Hypothetical protein At3g01050 [102782] (1 species)

    • Species Thale cress (Arabidopsis thaliana) [TaxId:3702] [102783] (1 PDB entry)

12. Interferon-induced 15 kDa protein [142936] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [142937] (1 PDB entry)
      Uniprot P05161 2-77! Uniprot P05161 78-153

13. Large proline-rich protein BAT3 [142952] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [142953] (1 PDB entry)
      Uniprot P46379 17-89

14. Nedd8 [54244] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [54245] (15 PDB entries)
      Uniprot Q15843

15. NEDD8 ultimate buster-1, NUB1 [117814] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [117815] (1 PDB entry)
      Uniprot Q9Y5A7 75-161

16. NPL4-like protein 1 [142934] (1 species)

    • Species Thale cress (Arabidopsis thaliana) [TaxId:3702] [142935] (1 PDB entry)
      Uniprot Q9LYC2 2-95

17. Rub1 [54248] (1 species)

    • Species Thale cress (Arabidopsis thaliana) [TaxId:3702] [54249] (1 PDB entry)

18. Splicing factor 3 subunit 1, C-terminal domain [117799] (3 species)

    1. Species Human (Homo sapiens) [TaxId:9606] [142931] (1 PDB entry)
       Uniprot Q15459 704-789

    2. Species Mouse (Mus musculus) [TaxId:10090] [117800] (1 PDB entry)
       Uniprot Q8K4Z5 685-786

    3. Species Thale cress (Arabidopsis thaliana) [TaxId:3702] [117801] (1 PDB entry)
       SQ Q8RXF1 683-780; T5E21.13/At1g14650

19. SUMO-1 (smt3 homologue) [54241] (3 species)

    1. Species Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId:4932] [54243] (3 PDB entries)

    2. Species Fruit fly (Drosophila melanogaster) [TaxId:7227] [256390] (1 PDB entry)

    3. Species Human (Homo sapiens) [TaxId:9606] [54242] (8 PDB entries)
       Uniprot Q93068

20. SUMO-2 [117816] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [117817] (8 PDB entries)
      Uniprot P61956

21. Tubulin-folding protein TbcE [117812] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [117813] (1 PDB entry)
      Uniprot Q8CIV8 441-524

22. Ubiquilin-3 [142946] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [142947] (2 PDB entries)
      Uniprot Q9H347 11-104! Uniprot Q9H347 15-98

23. Ubiquitin [54238] (7 species)

    1. Species African clawed frog (Xenopus laevis) [TaxId:8355] [224918] (1 PDB entry)

    2. Species Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId:4932] [89830] (9 PDB entries)

    3. Species Cow (Bos taurus) [TaxId:9913] [224919] (24 PDB entries)

    4. Species Human (Homo sapiens) [TaxId:9606] [54239] (126 PDB entries)
       Uniprot P62988
       identical sequence in many other species

    5. Species Mouse (Mus musculus) [TaxId:10090] [190020] (5 PDB entries)

    6. Species Norway rat (Rattus norvegicus) [TaxId:10116] [224920] (1 PDB entry)

    7. Species Synthetic, based on Saccharomyces cerevisiae sequence [54240] (1 PDB entry)

24. Ubiquitin carboxyl-terminal hydrolase 14 [117804] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [117805] (1 PDB entry)
      Uniprot Q9JMA1 3-85

25. Ubiquitin-like domain of parkin [89831] (2 species)

    1. Species Human (Homo sapiens) [TaxId:9606] [89832] (1 PDB entry)

    2. Species Mouse (Mus musculus) [TaxId:10090] [89833] (2 PDB entries)

26. Ubiquitin-like domain of Rad23 homolog A (Hhr23a) [102775] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [102776] (4 PDB entries)

27. Ubiquitin-like domain of Rad23 homolog B (Hhr23B) [102777] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [102778] (2 PDB entries)
      Uniprot P54727 1-82

28. Ubiquitin-like domain of tubulin folding cofactor B [102786] (2 species)

    1. Species Mouse (Mus musculus) [TaxId:10090] [117798] (1 PDB entry)
       Uniprot Q9D1E6 11-92

    2. Species Nematode (Caenorhabditis elegans) [TaxId:6239] [102787] (1 PDB entry)

29. Ubiquitin-like modifier protein hub1 [82579] (1 species)

    • Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [82580] (1 PDB entry)

30. Ubiquitin-like N-terminal domain of PLIC-2 [75358] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [75359] (1 PDB entry)

31. Ubiquitin-like PHD and RING finger domain-containing protein 1 [142948] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [142949] (1 PDB entry)
      Uniprot Q96T88 1-76

32. Ubiquitin-like PHD and RING finger domain-containing protein 2 [142944] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [142945] (1 PDB entry)
      Uniprot Q96PU4 1-76

33. Ubiquitin-like protein 3, Ubl3 [117806] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [117807] (1 PDB entry)
      Uniprot Q9Z2M6 1-103

34. Ubiquitin-like protein 3300001g02rik [102784] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [102785] (1 PDB entry)

35. Ubiquitin-like protein 5, ubl5 [102779] (2 species)

    1. Species Human (Homo sapiens) [TaxId:9606] [102780] (1 PDB entry)

    2. Species Mouse (Mus musculus) [TaxId:10090] [102781] (1 PDB entry)

36. Ubiquitin-like protein 7 [142942] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [142943] (1 PDB entry)
      Uniprot Q91W67 1-94

37. Ubiquitin-like protein bab25500 (2010008E23Rik) [117810] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [117811] (1 PDB entry)
      Uniprot Q9D8C5 163-244

38. Ubiquitin-like protein smt3a, SUMO-3 [142938] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [142939] (1 PDB entry)
      Uniprot P55854 14-92

39. automated matches [190118] (10 species)
    not a true protein

    1. Species African clawed frog (Xenopus laevis) [TaxId:8355] [255337] (1 PDB entry)

    2. Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [189675] (2 PDB entries)

    3. Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:559292] [193751] (4 PDB entries)

    4. Species Cow (Bos taurus) [TaxId:9913] [197078] (4 PDB entries)

    5. Species Entamoeba (Entamoeba histolytica) [TaxId:5759] [193323] (2 PDB entries)

    6. Species Human (Homo sapiens) [TaxId:9606] [189560] (70 PDB entries)

    7. Species Macaca fascicularis [TaxId:9541] [260502] (2 PDB entries)

    8. Species Mouse (Mus musculus) [TaxId:10090] [187278] (3 PDB entries)

    9. Species Paramecium tetraurelia strain d4-2 [TaxId:412030] [161334] (1 PDB entry)

    10. Species Schizosaccharomyces pombe [TaxId:284812] [196615] (2 PDB entries)

More info for Family d.15.1.1: Ubiquitin-related

Timeline for Family d.15.1.1: Ubiquitin-related:

• Family d.15.1.1: Ubiquitin-related first appeared (with stable ids) in SCOP 1.55
  
• Family d.15.1.1: Ubiquitin-related appears in SCOPe 2.03
  
• Family d.15.1.1: Ubiquitin-related appears in SCOPe 2.05
  
• Family d.15.1.1: Ubiquitin-related appears in the current release, SCOPe 2.08