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

  1. Root: SCOPe 2.08
  2. Class b: All beta proteins [48724] (180 folds)
  3. Fold b.1: Immunoglobulin-like beta-sandwich [48725] (33 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) (S)
  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
  2. B- and T-lymphocyte attenuator CD272 [158869] (1 species)
  3. Biliary glycoprotein C (CD66a, CEACAM1A[1,4]), N-terminal domain [81942] (1 species)
  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)
  7. CD28 [158865] (1 species)
    T-cell-specific surface glycoprotein
  8. CD4 V-set domains [48737] (2 species)
    1. Species Human (Homo sapiens) [TaxId:9606] [48738] (33 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
  11. CD86 (b7-2), N-terminal domain [63635] (1 species)
  12. Coxsackie virus and adenovirus receptor (Car), domain 1 [48730] (1 species)
  13. HSV glycoprotein D [63637] (1 species)
  14. Immunoglobulin heavy chain variable domain, VH [88543] (22 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] (67 PDB entries)
      SQ NA # humanized antidoby; bactericidal Fab-h6831 ! SQ NA # humanized antibody ! SQ NA # Humanized antibody ! SQ NA # engineered antibody
    3. Species Escherichia coli [TaxId:316407] [343346] (1 PDB entry)
    4. Species Human (Homo sapiens), cluster 1 [TaxId:9606] [88544] (37 PDB entries)
    5. Species Human (Homo sapiens), cluster 2.1 [TaxId:9606] [88545] (3 PDB entries)
    6. Species Human (Homo sapiens), cluster 2.2 [TaxId:9606] [88546] (2 PDB entries)
    7. Species Human (Homo sapiens), cluster 3 [TaxId:9606] [88547] (30 PDB entries)
      Uniprot Q6N089 20-243 # 95% sequence identity; natural chimera: antibody heavy chain (Fab HYB3)
    8. Species Human (Homo sapiens), cluster 4 [TaxId:9606] [101505] (4 PDB entries)
    9. Species Mouse (Mus musculus), cluster 1 [TaxId:10090] [88548] (68 PDB entries)
      Uniprot P01796 # ! HV27_MOUSE Ig heavy chain V-III region A4
    10. Species Mouse (Mus musculus), cluster 2.1 [TaxId:10090] [88549] (15 PDB entries)
      Uniprot P18527 # HV56_MOUSE Ig heavy chain V region 914; 90% sequence identity
    11. Species Mouse (Mus musculus), cluster 2.2 [TaxId:10090] [88550] (61 PDB entries)
      Uniprot P01811 # HV41_MOUSE (P01811) Ig heavy chain V region UPC10
    12. Species Mouse (Mus musculus), cluster 3.1 [TaxId:10090] [88551] (30 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)
    13. Species Mouse (Mus musculus), cluster 3.2 [TaxId:10090] [88552] (181 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
    14. Species Mouse (Mus musculus), cluster 3.3 [TaxId:10090] [88553] (1 PDB entry)
    15. 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
    16. Species Mouse (Mus musculus), cluster 5 [TaxId:10090] [88555] (36 PDB entries)
    17. Species Mouse (Mus musculus), cluster 6 [TaxId:10090] [88556] (12 PDB entries)
      SQ NA # part of Fab 28 against HIV-1 RT
    18. Species Mouse (Mus musculus), cluster 7.1 [TaxId:10090] [88557] (40 PDB entries)
      Uniprot P18532 # HV61_MOUSE Ig heavy chain V region 1B43 precursor
    19. Species Mouse (Mus musculus), cluster 7.2 [TaxId:10090] [88558] (32 PDB entries)
    20. Species Mouse (Mus musculus), cluster 7.3 [TaxId:10090] [88559] (2 PDB entries)
    21. Species Norway rat (Rattus norvegicus) [TaxId:10116] [88560] (16 PDB entries)
    22. 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] (60 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] (132 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] (51 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] (42 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] (231 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] (14 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] (8 PDB entries)
      Uniprot Q8N355 20-230 # 94% sequence identity; natural chimera: antibody light chain (Fab HYB3)
    8. Species Mouse (Mus musculus) [TaxId:10090] [88541] (36 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] (9 PDB entries)
    2. Species Mouse (Mus musculus) [TaxId:10090] [48941] (3 PDB entries)
  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)
  20. Myelin membrane adhesion molecule P0 [48728] (1 species)
  21. Myelin oligodendrocyte glycoprotein (MOG) [89174] (1 species)
  22. N-terminal domain of sialic acid binding Ig-like lectin 7 (SIGLEC-7, p75/AIRM1) [89176] (1 species)
  23. N-terminal domain of sialoadhesin [48732] (1 species)
  24. NK cell activating receptor NKP44 [89178] (1 species)
    a triggering partner in natural cytotoxicity
  25. Novel antigen receptor (against lysozyme) [110042] (1 species)
  26. Novel antigen receptor 12Y-1 [110044] (1 species)
  27. Novel antigen receptor 12Y-2 [110046] (1 species)
  28. Polymeric-immunoglobulin receptor, PIGR [117038] (1 species)
  29. Programmed cell death protein 1, PD1, extracellular domain [101510] (2 species)
    1. Species Human (Homo sapiens) [TaxId:9606] [256383] (17 PDB entries)
    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] (30 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] (22 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)
  33. automated matches [190119] (23 species)
    not a true protein
    1. Species Camel (Camelus dromedarius) [TaxId:9838] [187219] (42 PDB entries)
    2. Species Camelus bactrianus [TaxId:9837] [371849] (5 PDB entries)
    3. Species Cow (Bos taurus) [TaxId:9913] [197337] (3 PDB entries)
    4. Species Dogfish (Squalus acanthias) [TaxId:7797] [226656] (2 PDB entries)
    5. Species Escherichia coli [TaxId:83333] [354477] (1 PDB entry)
    6. Species Human herpesvirus 1 [TaxId:10299] [256116] (1 PDB entry)
    7. Species Human herpesvirus 2 [TaxId:10313] [259821] (1 PDB entry)
    8. Species Human herpesvirus 2 [TaxId:10315] [256151] (1 PDB entry)
    9. Species Llama (Lama glama) [TaxId:9844] [187485] (227 PDB entries)
    10. Species Llama glama [TaxId:9844] [236993] (3 PDB entries)
    11. Species Macaca mulatta [TaxId:9541] [188468] (1 PDB entry)
    12. Species Rhesus monkey (Macaca mulatta) [TaxId:9544] [377132] (6 PDB entries)
    13. Species Norway rat (Rattus norvegicus) [TaxId:10116] [187415] (25 PDB entries)
    14. Species Nurse shark (Ginglymostoma cirratum) [TaxId:7801] [187220] (4 PDB entries)
    15. Species Ornithorhynchus anatinus [TaxId:9258] [228732] (1 PDB entry)
    16. Species Pig (Sus scrofa) [TaxId:9823] [322548] (1 PDB entry)
    17. Species Rabbit (Oryctolagus cuniculus) [TaxId:9986] [331472] (6 PDB entries)
    18. Species Rat (Rattus rattus) [TaxId:10117] [225551] (1 PDB entry)
    19. Species Spotted wobbegong (Orectolobus maculatus) [TaxId:168098] [187564] (9 PDB entries)
    20. Species Vicugna pacos [TaxId:30538] [189756] (80 PDB entries)
    21. Species Human (Homo sapiens) [TaxId:9606] [188740] (689 PDB entries)
    22. Species Cricetulus migratorius [TaxId:10032] [419867] (1 PDB entry)
    23. Species Mouse (Mus musculus) [TaxId:10090] [186842] (610 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):