SCOPe 2.04: 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: SCOPe 2.04

2. Class b: All beta proteins [48724] (176 folds)

3. Fold b.1: Immunoglobulin-like beta-sandwich [48725] (31 superfamilies)
   sandwich; 7 strands in 2 sheets; greek-key
   some members of the fold have additional strands

4. Superfamily b.1.1: Immunoglobulin [48726] (5 families)

5. Family b.1.1.1: V set domains (antibody variable domain-like) [48727] (33 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)
     Uniprot P04488 218-394! Uniprot P04488 220-390

2. B- and T-lymphocyte attenuator CD272 [158869] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [158870] (1 PDB entry)
     Uniprot Q7Z6A9 34-137

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

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

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

   1. Species Camel (Camelus dromedarius) [TaxId:9838] [88564] (19 PDB entries)
      SQ NA # camelid antibody

   2. Species Human (Homo sapiens) [TaxId:9606] [158863] (2 PDB entries)

   3. Species Llama (Lama glama) [TaxId:9844] [88565] (7 PDB entries)

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

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

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

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

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

7. CD28 [158865] (1 species)
   T-cell-specific surface glycoprotein

   • Species Human (Homo sapiens) [TaxId:9606] [158866] (1 PDB entry)
     Uniprot P10747 19-136

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

   1. Species Human (Homo sapiens) [TaxId:9606] [48738] (31 PDB entries)

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

9. CD8 [48734] (3 species)

   1. Species Human (Homo sapiens) [TaxId:9606] [48735] (3 PDB entries)

   2. Species Mouse (Mus musculus) [TaxId:10090] [48736] (5 PDB entries)

   3. Species Mouse (Mus musculus), beta-chain [TaxId:10090] [158864] (2 PDB entries)
      Uniprot P10300 22-136

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

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

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

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

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

    • Species Human (Homo sapiens) [TaxId:9606] [48731] (7 PDB entries)

13. 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

14. Immunoglobulin heavy chain variable domain, VH [88543] (21 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 Chinese hamster (Cricetulus griseus) [TaxId:10029] [88561] (1 PDB entry)

    2. Species Engineered (including hybrid species) [88562] (68 PDB entries)
       SQ NA # humanized antidoby; bactericidal Fab-h6831 ! SQ NA # humanized antibody ! SQ NA # Humanized antibody ! SQ NA # engineered antibody

    3. Species Human (Homo sapiens), cluster 1 [TaxId:9606] [88544] (37 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] (2 PDB entries)

    6. Species Human (Homo sapiens), cluster 3 [TaxId:9606] [88547] (33 PDB entries)
       Uniprot Q6N089 20-243 # 95% sequence identity; natural chimera: antibody heavy chain (Fab HYB3)

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

    8. Species Mouse (Mus musculus), cluster 1 [TaxId:10090] [88548] (57 PDB entries)
       Uniprot P01796 # ! HV27_MOUSE Ig heavy chain V-III region A4

    9. Species Mouse (Mus musculus), cluster 2.1 [TaxId:10090] [88549] (14 PDB entries)
       Uniprot P18527 # HV56_MOUSE Ig heavy chain V region 914; 90% sequence identity

    10. Species Mouse (Mus musculus), cluster 2.2 [TaxId:10090] [88550] (58 PDB entries)
        Uniprot P01811 # HV41_MOUSE (P01811) Ig heavy chain V region UPC10

    11. Species Mouse (Mus musculus), cluster 3.1 [TaxId:10090] [88551] (31 PDB entries)
        SQ NA # natural chimera; best hits are: Uniprot P01751 (Ig heavy chain V region B1-8/186-2) and Uniprot P01864 (Ig gamma-2A chain C region secreted form)

    12. Species Mouse (Mus musculus), cluster 3.2 [TaxId:10090] [88552] (178 PDB entries)
        Uniprot P01756 1-117 # 78% sequense identity; HV12_MOUSE Ig heavy chain V region MOPC 104E ! SQ NA # humanized antibody ! Uniprot P01750 # HV06_MOUSE Ig heavy chain V region 102 precursor ! Uniprot P01750 20-116 # ! HV06_MOUSE Ig heavy chain V region 102 precursor

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

    14. Species Mouse (Mus musculus), cluster 4 [TaxId:10090] [88554] (34 PDB entries)
        Uniprot P06327 20-117 # HV52_MOUSE (P06327) Ig heavy chain V region VH558 A1/A4 precursor; 57% sequence identity ! Uniprot P01631 # KV2G_MOUSE (P01631) Ig kappa chain V-II region 26-10

    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)
        SQ NA # part of Fab 28 against HIV-1 RT

    17. Species Mouse (Mus musculus), cluster 7.1 [TaxId:10090] [88557] (39 PDB entries)
        Uniprot P18532 # HV61_MOUSE Ig heavy chain V region 1B43 precursor

    18. Species Mouse (Mus musculus), cluster 7.2 [TaxId:10090] [88558] (31 PDB entries)

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

    20. Species Norway rat (Rattus norvegicus) [TaxId:10116] [88560] (16 PDB entries)

    21. Species Synthetic construct [TaxId:32630] [158862] (3 PDB entries)

15. Immunoglobulin light chain kappa variable domain, VL-kappa [88519] (16 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] (61 PDB entries)
       SQ NA # humanized antidoby; bactericidal Fab-h6831 ! SQ NA # Humanized antibody ! SQ NA # humanized antibody ! SQ NA # engineered antibody

    2. Species Escherichia coli [TaxId:562] [224853] (1 PDB entry)

    3. Species Human (Homo sapiens), cluster 1 [TaxId:9606] [88520] (19 PDB entries)

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

    5. Species Human (Homo sapiens), cluster 3.1 [TaxId:9606] [88522] (8 PDB entries)

    6. Species Human (Homo sapiens), cluster 3.2 [TaxId:9606] [88523] (31 PDB entries)

    7. Species Mouse (Mus musculus), cluster 1.1 [TaxId:10090] [88524] (131 PDB entries)
       Uniprot P01631 #KV2G_MOUSE Ig kappa chain V-II region 26-10; 79% sequence identity ! Uniprot P06310 # KV2F_HUMAN IG KAPPA CHAIN V-II REGION RPMI 6410 PRECURSOR ! Uniprot P03976 # KV2E_MOUSE (P03976) Ig kappa chain V-II region 17S29.1 ! Uniprot P01642 21-115 # ! KV2G_MOUSE IG KAPPA CHAIN V-II REGION 26-10

    8. Species Mouse (Mus musculus), cluster 1.2 [TaxId:10090] [88525] (46 PDB entries)

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

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

    11. Species Mouse (Mus musculus), cluster 3.2 [TaxId:10090] [88528] (40 PDB entries)
        Uniprot P04940 # KV6F_MOUSE IG KAPPA CHAIN V-VI REGION NQ2-17.4.1

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

    13. Species Mouse (Mus musculus), cluster 3.4 [TaxId:10090] [88530] (4 PDB entries)

    14. Species Mouse (Mus musculus), cluster 4 [TaxId:10090] [88531] (213 PDB entries)
        Uniprot P01645 1-106 # 95% sequense identity; KV5L_MOUSE Ig kappa chain V-V region HP 93G7 ! SQ NA # natural chimera; best hits are: Uniprot P01637 (Ig kappa chain V-V region T1) and Uniprot P01837 (Ig kappa chain C region) ! SQ NA # humanized antibody ! SQ NA # part of Fab 28 against HIV-1 RT ! Uniprot P01642 21-115 # ! KV5I_MOUSE Ig kappa chain V-V region L7 precursor

    15. Species Norway rat (Rattus norvegicus) [TaxId:10116] [88532] (9 PDB entries)

    16. Species Synthetic construct [TaxId:32630] [158859] (2 PDB entries)

16. 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 Chinese hamster (Cricetulus griseus) [TaxId:10029] [88542] (1 PDB entry)

    2. Species Human (Homo sapiens), cluster 1 [TaxId:9606] [88535] (4 PDB entries)
       SQ NA # Bence-Jones protein JTO ! Uniprot P06317 # Ig lambda chain V-VI region SUT

    3. Species Human (Homo sapiens), cluster 2 [TaxId:9606] [88536] (10 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] (7 PDB entries)
       Uniprot Q8N355 20-230 # 94% sequence identity; natural chimera: antibody light chain (Fab HYB3)

    8. Species Mouse (Mus musculus) [TaxId:10090] [88541] (35 PDB entries)

    9. Species Norway rat (Rattus norvegicus) [TaxId:10116] [101504] (7 PDB entries)

17. 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)

18. 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)

19. Kin of IRRE-like protein 3, KIRREL3 [158867] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [158868] (1 PDB entry)
      Uniprot Q8IZU9 413-521

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

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

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

    • Species Norway rat (Rattus norvegicus) [TaxId:10116] [89175] (4 PDB entries)

22. 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)

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

    • Species Mouse (Mus musculus) [TaxId:10090] [48733] (6 PDB entries)
      Uniprot Q62230 20-130

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

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

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

    • Species Nurse shark (Ginglymostoma cirratum) [TaxId:7801] [110043] (3 PDB entries)
      Uniprot Q8AXI4 # fragment

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

    • Species Spotted wobbegong (Orectolobus maculatus) [TaxId:168098] [110045] (1 PDB entry)
      Uniprot Q6X1E7 # fragment

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

    • Species Spotted wobbegong (Orectolobus maculatus) [TaxId:168098] [110047] (1 PDB entry)
      Uniprot Q6X1E6 # fragment

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

    • Species Human (Homo sapiens) [TaxId:9606] [117039] (1 PDB entry)
      Uniprot P01833 20-127 # N-terminal, ligand-binding domain

29. Programmed cell death protein 1, PD1, extracellular domain [101510] (2 species)

    1. Species Human (Homo sapiens) [TaxId:9606] [256383] (1 PDB entry)

    2. Species Mouse (Mus musculus) [TaxId:10090] [101511] (5 PDB entries)

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

    1. Species Human (Homo sapiens), alpha-chain [TaxId:9606] [48935] (21 PDB entries)

    2. Species Human (Homo sapiens), beta-chain [TaxId:9606] [48937] (29 PDB entries)

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

    4. Species Human (Homo sapiens), gamma-chain [TaxId:9606] [63651] (3 PDB entries)

    5. Species Mouse (Mus musculus), alpha-chain [TaxId:10090] [48934] (21 PDB entries)

    6. Species Mouse (Mus musculus), beta-chain [TaxId:10090] [48936] (28 PDB entries)

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

    1. Species Human (Homo sapiens) [TaxId:9606] [101507] (2 PDB entries)
       Uniprot Q9NP99 21-133

    2. Species Mouse (Mus musculus) [TaxId:10090] [117037] (1 PDB entry)
       Uniprot Q9JKE2 25-134

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

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

33. automated matches [190119] (19 species)
    not a true protein

    1. Species Camel (Camelus dromedarius) [TaxId:9838] [187219] (22 PDB entries)

    2. Species Canis lupus [TaxId:9615] [257003] (1 PDB entry)

    3. Species Cow (Bos taurus) [TaxId:9913] [197337] (1 PDB entry)

    4. Species Dogfish (Squalus acanthias) [TaxId:7797] [226656] (2 PDB entries)

    5. Species Escherichia coli [TaxId:562] [259457] (1 PDB entry)

    6. Species Human (Homo sapiens) [TaxId:9606] [188740] (96 PDB entries)

    7. Species Human herpesvirus 1 [TaxId:10299] [256116] (1 PDB entry)

    8. Species Human herpesvirus 2 [TaxId:10313] [259821] (1 PDB entry)

    9. Species Human herpesvirus 2 [TaxId:10315] [256151] (1 PDB entry)

    10. Species Llama (Lama glama) [TaxId:9844] [187485] (76 PDB entries)

    11. Species Llama glama [TaxId:9844] [236993] (1 PDB entry)

    12. Species Macaca mulatta [TaxId:9541] [188468] (1 PDB entry)

    13. Species Mouse (Mus musculus) [TaxId:10090] [186842] (122 PDB entries)

    14. Species Norway rat (Rattus norvegicus) [TaxId:10116] [187415] (7 PDB entries)

    15. Species Nurse shark (Ginglymostoma cirratum) [TaxId:7801] [187220] (4 PDB entries)

    16. Species Ornithorhynchus anatinus [TaxId:9258] [228732] (1 PDB entry)

    17. Species Rat (Rattus rattus) [TaxId:10117] [225551] (1 PDB entry)

    18. Species Spotted wobbegong (Orectolobus maculatus) [TaxId:168098] [187564] (5 PDB entries)

    19. Species Vicugna pacos [TaxId:30538] [189756] (6 PDB entries)

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 SCOPe 2.03
  
• Family b.1.1.1: V set domains (antibody variable domain-like) appears in SCOPe 2.05
  
• Family b.1.1.1: V set domains (antibody variable domain-like) appears in the current release, SCOPe 2.08