SCOP 1.73: Family b.1.1.1: V set domains (antibody variable domain-like)

Lineage for Family b.1.1.1: V set domains (antibody variable domain-like)

1. Root: SCOP 1.73

2. Class b: All beta proteins [48724] (165 folds)

3. Fold b.1: Immunoglobulin-like beta-sandwich [48725] (27 superfamilies)
   sandwich; 7 strands in 2 sheets; greek-key
   some members of the fold have additional strands

4. Superfamily b.1.1: Immunoglobulin [48726] (4 families)

5. Family b.1.1.1: V set domains (antibody variable domain-like) [48727] (29 proteins)

Proteins:

1. Alphaherpesvirus glycoprotein E [141008] (1 species)
   elaborated with insertions and C-terminal extensions

   • Species Human herpesvirus 1 [TaxId:10298] [141009] (2 PDB entries)

2. Biliary glycoprotein C (CD66a, CEACAM1A[1,4]), N-terminal domain [81942] (1 species)

   • Species Mouse (Mus musculus) [TaxId:10090] [81943] (1 PDB entry)

3. Camelid IG heavy chain variable domain, VHh [88563] (2 species)

   1. Species Camel (Camelus dromedarius) [TaxId:9838] [88564] (13 PDB entries)

   2. Species Llama (Lama glama) [TaxId:9844] [88565] (8 PDB entries)

4. CD2, first domain [48740] (2 species)

   1. Species Human (Homo sapiens) [TaxId:9606] [48741] (4 PDB entries)

   2. Species Rat (Rattus norvegicus) [TaxId:10116] [48742] (5 PDB entries)

5. CD2-binding domain of CD58, N-terminal domain [48743] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [48744] (3 PDB entries)

6. CD4 V-set domains [48737] (2 species)

   1. Species Human (Homo sapiens) [TaxId:9606] [48738] (25 PDB entries)

   2. Species Rat (Rattus rattus) [TaxId:10117] [48739] (1 PDB entry)

7. CD8 [48734] (2 species)

   1. Species Human (Homo sapiens) [TaxId:9606] [48735] (2 PDB entries)

   2. Species Mouse (Mus musculus) [TaxId:10090] [48736] (4 PDB entries)

8. CD80, N-terminal domain [48745] (1 species)
   a soluble form of b7-1

   • Species Human (Homo sapiens) [TaxId:9606] [48746] (2 PDB entries)

9. CD86 (b7-2), N-terminal domain [63635] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [63636] (2 PDB entries)

10. Coxsackie virus and adenovirus receptor (Car), domain 1 [48730] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [48731] (8 PDB entries)

11. HSV glycoprotein D [63637] (1 species)

    • Species Herpes simplex virus type 1 [TaxId:10298] [63638] (2 PDB entries)
      elaborated with insertions and N- and C-terminal extensions

12. Immunoglobulin heavy chain variable domain, VH [88543] (20 species)
    VH domains of human and mouse antibodies are clustered by the sequence similarity within the germline encoded segment and then by the size of the complementarity determining regions CDR1 and CDR2, so the clusters may correspond to putative germline families in the species genomes; VH domains with artificial or grafted exogenous CDRs are listed as engineered species

    1. Species Engineered (including hybrid species) [88562] (66 PDB entries)

    2. Species Hamster (Cricetulus griseus) [TaxId:10029] [88561] (1 PDB entry)

    3. Species Human (Homo sapiens), cluster 1 [TaxId:9606] [88544] (33 PDB entries)

    4. Species Human (Homo sapiens), cluster 2.1 [TaxId:9606] [88545] (3 PDB entries)

    5. Species Human (Homo sapiens), cluster 2.2 [TaxId:9606] [88546] (1 PDB entry)

    6. Species Human (Homo sapiens), cluster 3 [TaxId:9606] [88547] (19 PDB entries)

    7. Species Human (Homo sapiens), cluster 4 [TaxId:9606] [101505] (2 PDB entries)

    8. Species Mouse (Mus musculus), cluster 1 [TaxId:10090] [88548] (43 PDB entries)

    9. Species Mouse (Mus musculus), cluster 2.1 [TaxId:10090] [88549] (16 PDB entries)

    10. Species Mouse (Mus musculus), cluster 2.2 [TaxId:10090] [88550] (51 PDB entries)

    11. Species Mouse (Mus musculus), cluster 3.1 [TaxId:10090] [88551] (34 PDB entries)

    12. Species Mouse (Mus musculus), cluster 3.2 [TaxId:10090] [88552] (148 PDB entries)

    13. Species Mouse (Mus musculus), cluster 3.3 [TaxId:10090] [88553] (1 PDB entry)

    14. Species Mouse (Mus musculus), cluster 4 [TaxId:10090] [88554] (32 PDB entries)

    15. Species Mouse (Mus musculus), cluster 5 [TaxId:10090] [88555] (36 PDB entries)

    16. Species Mouse (Mus musculus), cluster 6 [TaxId:10090] [88556] (12 PDB entries)

    17. Species Mouse (Mus musculus), cluster 7.1 [TaxId:10090] [88557] (36 PDB entries)

    18. Species Mouse (Mus musculus), cluster 7.2 [TaxId:10090] [88558] (22 PDB entries)

    19. Species Mouse (Mus musculus), cluster 7.3 [TaxId:10090] [88559] (2 PDB entries)

    20. Species Rat (Rattus norvegicus) [TaxId:10116] [88560] (15 PDB entries)

13. Immunoglobulin light chain kappa variable domain, VL-kappa [88519] (14 species)
    VL-kappa domains of human and mouse antibodies are clustered by the sequence similarity within the germline encoded segment and then by the size of the complementarity determining regions CDR1 and CDR2, so the clusters may correspond to putative germline families in the species genomes; VL-kappa domains with artificial or grafted exogenous CDRs are listed as engineered species

    1. Species Engineered (including hybrid species) [88533] (52 PDB entries)

    2. Species Human (Homo sapiens), cluster 1 [TaxId:9606] [88520] (18 PDB entries)

    3. Species Human (Homo sapiens), cluster 2 [TaxId:9606] [88521] (10 PDB entries)

    4. Species Human (Homo sapiens), cluster 3.1 [TaxId:9606] [88522] (7 PDB entries)

    5. Species Human (Homo sapiens), cluster 3.2 [TaxId:9606] [88523] (29 PDB entries)

    6. Species Mouse (Mus musculus), cluster 1.1 [TaxId:10090] [88524] (127 PDB entries)

    7. Species Mouse (Mus musculus), cluster 1.2 [TaxId:10090] [88525] (35 PDB entries)

    8. Species Mouse (Mus musculus), cluster 2 [TaxId:10090] [88526] (28 PDB entries)

    9. Species Mouse (Mus musculus), cluster 3.1 [TaxId:10090] [88527] (13 PDB entries)

    10. Species Mouse (Mus musculus), cluster 3.2 [TaxId:10090] [88528] (40 PDB entries)

    11. Species Mouse (Mus musculus), cluster 3.3 [TaxId:10090] [88529] (2 PDB entries)

    12. Species Mouse (Mus musculus), cluster 3.4 [TaxId:10090] [88530] (3 PDB entries)

    13. Species Mouse (Mus musculus), cluster 4 [TaxId:10090] [88531] (181 PDB entries)

    14. Species Rat (Rattus norvegicus) [TaxId:10116] [88532] (8 PDB entries)

14. Immunoglobulin light chain lambda variable domain, VL-lambda [88534] (9 species)
    VL-lambda domains of human antibodies are clustered by the sequence similarity within the germline encoded segment and then by the size of the complementarity determining regions CDR1 and CDR2, so the clusters may correspond to putative germline families in the human genome; mouse VL-lambda domains belong to a single germline family

    1. Species Hamster (Cricetulus griseus) [TaxId:10029] [88542] (1 PDB entry)

    2. Species Human (Homo sapiens), cluster 1 [TaxId:9606] [88535] (4 PDB entries)

    3. Species Human (Homo sapiens), cluster 2 [TaxId:9606] [88536] (9 PDB entries)

    4. Species Human (Homo sapiens), cluster 3.1 [TaxId:9606] [88537] (1 PDB entry)

    5. Species Human (Homo sapiens), cluster 3.2 [TaxId:9606] [88538] (1 PDB entry)

    6. Species Human (Homo sapiens), cluster 4 [TaxId:9606] [88539] (23 PDB entries)

    7. Species Human (Homo sapiens), cluster 5 [TaxId:9606] [88540] (5 PDB entries)

    8. Species Mouse (Mus musculus) [TaxId:10090] [88541] (33 PDB entries)

    9. Species Rat (Rattus norvegicus) [TaxId:10116] [101504] (8 PDB entries)

15. Immunoreceptor CTLA-4 (CD152), N-terminal fragment [48939] (2 species)

    1. Species Human (Homo sapiens) [TaxId:9606] [48940] (3 PDB entries)

    2. Species Mouse (Mus musculus) [TaxId:10090] [48941] (1 PDB entry)

16. Junction adhesion molecule, JAM, N-terminal domain [48747] (2 species)

    1. Species Human (Homo sapiens) [TaxId:9606] [89180] (1 PDB entry)

    2. Species Mouse (Mus musculus) [TaxId:10090] [48748] (1 PDB entry)

17. Myelin membrane adhesion molecule P0 [48728] (1 species)

    • Species Rat (Rattus norvegicus) [TaxId:10116] [48729] (1 PDB entry)

18. Myelin oligodendrocyte glycoprotein (MOG) [89174] (1 species)

    • Species Rat (Rattus norvegicus) [TaxId:10116] [89175] (3 PDB entries)

19. N-terminal domain of sialic acid binding Ig-like lectin 7 (SIGLEC-7, p75/AIRM1) [89176] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [89177] (6 PDB entries)

20. N-terminal domain of sialoadhesin [48732] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [48733] (7 PDB entries)

21. NK cell activating receptor NKP44 [89178] (1 species)
    a triggering partner in natural cytotoxicity

    • Species Human (Homo sapiens) [TaxId:9606] [89179] (1 PDB entry)

22. Novel antigen receptor (against lysozyme) [110042] (1 species)

    • Species Nurse shark (Ginglymostoma cirratum) [TaxId:7801] [110043] (2 PDB entries)

23. Novel antigen receptor 12Y-1 [110044] (1 species)

    • Species Spotted wobbegong (Orectolobus maculatus) [TaxId:168098] [110045] (1 PDB entry)

24. Novel antigen receptor 12Y-2 [110046] (1 species)

    • Species Spotted wobbegong (Orectolobus maculatus) [TaxId:168098] [110047] (1 PDB entry)

25. Polymeric-immunoglobulin receptor, PIGR [117038] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [117039] (1 PDB entry)

26. Programmed cell death protein 1, PD1, extracellular domain [101510] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [101511] (1 PDB entry)

27. T-cell antigen receptor [48933] (6 species)
    sequences may differ within each classified species

    1. Species Human (Homo sapiens), alpha-chain [TaxId:9606] [48935] (10 PDB entries)

    2. Species Human (Homo sapiens), beta-chain [TaxId:9606] [48937] (16 PDB entries)

    3. Species Human (Homo sapiens), delta-chain [TaxId:9606] [48938] (2 PDB entries)

    4. Species Human (Homo sapiens), gamma-chain [TaxId:9606] [63651] (1 PDB entry)

    5. Species Mouse (Mus musculus), alpha-chain [TaxId:10090] [48934] (17 PDB entries)

    6. Species Mouse (Mus musculus), beta-chain [TaxId:10090] [48936] (19 PDB entries)

28. TREM-1 (triggering receptor expressed on myeloid cells 1) [101506] (2 species)

    1. Species Human (Homo sapiens) [TaxId:9606] [101507] (2 PDB entries)

    2. Species Mouse (Mus musculus) [TaxId:10090] [117037] (1 PDB entry)

29. Tyrosine-protein kinase receptor tyro3, N-terminal domain [101508] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [101509] (1 PDB entry)

More info for Family b.1.1.1: V set domains (antibody variable domain-like)

Timeline for Family b.1.1.1: V set domains (antibody variable domain-like):

• Family b.1.1.1: V set domains (antibody variable domain-like) first appeared (with stable ids) in SCOP 1.55
  
• Family b.1.1.1: V set domains (antibody variable domain-like) appears in SCOP 1.71
  
• Family b.1.1.1: V set domains (antibody variable domain-like) appears in SCOP 1.75
  
• Family b.1.1.1: V set domains (antibody variable domain-like) appears in the current release, SCOPe 2.08