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

  1. Root: SCOPe 2.05
  2. 1755445Class b: All beta proteins [48724] (176 folds)
  3. 1755446Fold 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. 1755447Superfamily b.1.1: Immunoglobulin [48726] (5 families) (S)
  5. 1755448Family b.1.1.1: V set domains (antibody variable domain-like) [48727] (33 protein domains)

Protein Domains:

  1. 1755449Alphaherpesvirus glycoprotein E [141008] (1 species)
    elaborated with insertions and C-terminal extensions
  2. 1755455B- and T-lymphocyte attenuator CD272 [158869] (1 species)
  3. 1755459Biliary glycoprotein C (CD66a, CEACAM1A[1,4]), N-terminal domain [81942] (1 species)
  4. 1755462Camelid IG heavy chain variable domain, VHh [88563] (3 species)
    1. 1755463Species Camel (Camelus dromedarius) [TaxId:9838] [88564] (19 PDB entries)
      SQ NA # camelid antibody
    2. 1755497Species Human (Homo sapiens) [TaxId:9606] [158863] (2 PDB entries)
    3. 1755502Species Llama (Lama glama) [TaxId:9844] [88565] (7 PDB entries)
  5. 1755511CD2, first domain [48740] (2 species)
    1. 1755512Species Human (Homo sapiens) [TaxId:9606] [48741] (4 PDB entries)
    2. 1755518Species Norway rat (Rattus norvegicus) [TaxId:10116] [48742] (5 PDB entries)
  6. 1755531CD2-binding domain of CD58, N-terminal domain [48743] (1 species)
  7. 1755537CD28 [158865] (1 species)
    T-cell-specific surface glycoprotein
  8. 1755540CD4 V-set domains [48737] (2 species)
    1. 1755541Species Human (Homo sapiens) [TaxId:9606] [48738] (31 PDB entries)
    2. 1755584Species Rat (Rattus rattus) [TaxId:10117] [48739] (1 PDB entry)
  9. 1755586CD8 [48734] (3 species)
    1. 1755587Species Human (Homo sapiens) [TaxId:9606] [48735] (3 PDB entries)
    2. 1755595Species Mouse (Mus musculus) [TaxId:10090] [48736] (5 PDB entries)
    3. 1755608Species Mouse (Mus musculus), beta-chain [TaxId:10090] [158864] (2 PDB entries)
      Uniprot P10300 22-136
  10. 1755613CD80, N-terminal domain [48745] (1 species)
    a soluble form of b7-1
  11. 1755618CD86 (b7-2), N-terminal domain [63635] (1 species)
  12. 1755624Coxsackie virus and adenovirus receptor (Car), domain 1 [48730] (1 species)
  13. 1755646HSV glycoprotein D [63637] (1 species)
  14. 1755653Immunoglobulin 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. 1755654Species Chinese hamster (Cricetulus griseus) [TaxId:10029] [88561] (1 PDB entry)
    2. 1755657Species 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. 1755760Species Human (Homo sapiens), cluster 1 [TaxId:9606] [88544] (37 PDB entries)
    4. 1755821Species Human (Homo sapiens), cluster 2.1 [TaxId:9606] [88545] (3 PDB entries)
    5. 1755827Species Human (Homo sapiens), cluster 2.2 [TaxId:9606] [88546] (2 PDB entries)
    6. 1755830Species 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. 1755902Species Human (Homo sapiens), cluster 4 [TaxId:9606] [101505] (4 PDB entries)
    8. 1755910Species Mouse (Mus musculus), cluster 1 [TaxId:10090] [88548] (63 PDB entries)
      Uniprot P01796 # ! HV27_MOUSE Ig heavy chain V-III region A4
    9. 1755994Species 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. 1756016Species Mouse (Mus musculus), cluster 2.2 [TaxId:10090] [88550] (58 PDB entries)
      Uniprot P01811 # HV41_MOUSE (P01811) Ig heavy chain V region UPC10
    11. 1756105Species 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. 1756146Species 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. 1756374Species Mouse (Mus musculus), cluster 3.3 [TaxId:10090] [88553] (1 PDB entry)
    14. 1756377Species 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. 1756427Species Mouse (Mus musculus), cluster 5 [TaxId:10090] [88555] (36 PDB entries)
    16. 1756475Species Mouse (Mus musculus), cluster 6 [TaxId:10090] [88556] (12 PDB entries)
      SQ NA # part of Fab 28 against HIV-1 RT
    17. 1756490Species Mouse (Mus musculus), cluster 7.1 [TaxId:10090] [88557] (39 PDB entries)
      Uniprot P18532 # HV61_MOUSE Ig heavy chain V region 1B43 precursor
    18. 1756539Species Mouse (Mus musculus), cluster 7.2 [TaxId:10090] [88558] (31 PDB entries)
    19. 1756574Species Mouse (Mus musculus), cluster 7.3 [TaxId:10090] [88559] (2 PDB entries)
    20. 1756577Species Norway rat (Rattus norvegicus) [TaxId:10116] [88560] (16 PDB entries)
    21. 1756610Species Synthetic construct [TaxId:32630] [158862] (3 PDB entries)
  15. 1756616Immunoglobulin 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. 1756617Species 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. 1756699Species Escherichia coli [TaxId:562] [224853] (1 PDB entry)
    3. 1756701Species Human (Homo sapiens), cluster 1 [TaxId:9606] [88520] (19 PDB entries)
    4. 1756745Species Human (Homo sapiens), cluster 2 [TaxId:9606] [88521] (10 PDB entries)
    5. 1756761Species Human (Homo sapiens), cluster 3.1 [TaxId:9606] [88522] (8 PDB entries)
    6. 1756776Species Human (Homo sapiens), cluster 3.2 [TaxId:9606] [88523] (31 PDB entries)
    7. 1756839Species 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. 1757008Species Mouse (Mus musculus), cluster 1.2 [TaxId:10090] [88525] (46 PDB entries)
    9. 1757072Species Mouse (Mus musculus), cluster 2 [TaxId:10090] [88526] (28 PDB entries)
    10. 1757113Species Mouse (Mus musculus), cluster 3.1 [TaxId:10090] [88527] (13 PDB entries)
    11. 1757132Species 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. 1757200Species Mouse (Mus musculus), cluster 3.3 [TaxId:10090] [88529] (2 PDB entries)
    13. 1757204Species Mouse (Mus musculus), cluster 3.4 [TaxId:10090] [88530] (4 PDB entries)
    14. 1757209Species 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. 1757477Species Norway rat (Rattus norvegicus) [TaxId:10116] [88532] (9 PDB entries)
    16. 1757495Species Synthetic construct [TaxId:32630] [158859] (2 PDB entries)
  16. 1757501Immunoglobulin 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. 1757502Species Chinese hamster (Cricetulus griseus) [TaxId:10029] [88542] (1 PDB entry)
    2. 1757505Species 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. 1757514Species Human (Homo sapiens), cluster 2 [TaxId:9606] [88536] (10 PDB entries)
    4. 1757529Species Human (Homo sapiens), cluster 3.1 [TaxId:9606] [88537] (1 PDB entry)
    5. 1757531Species Human (Homo sapiens), cluster 3.2 [TaxId:9606] [88538] (1 PDB entry)
    6. 1757533Species Human (Homo sapiens), cluster 4 [TaxId:9606] [88539] (23 PDB entries)
    7. 1757579Species 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. 1757592Species Mouse (Mus musculus) [TaxId:10090] [88541] (35 PDB entries)
    9. 1757640Species Norway rat (Rattus norvegicus) [TaxId:10116] [101504] (7 PDB entries)
  17. 1757661Immunoreceptor CTLA-4 (CD152), N-terminal fragment [48939] (2 species)
    1. 1757662Species Human (Homo sapiens) [TaxId:9606] [48940] (3 PDB entries)
    2. 1757668Species Mouse (Mus musculus) [TaxId:10090] [48941] (2 PDB entries)
  18. 1757674Junction adhesion molecule, JAM, N-terminal domain [48747] (2 species)
    1. 1757675Species Human (Homo sapiens) [TaxId:9606] [89180] (1 PDB entry)
    2. 1757678Species Mouse (Mus musculus) [TaxId:10090] [48748] (1 PDB entry)
  19. 1757680Kin of IRRE-like protein 3, KIRREL3 [158867] (1 species)
  20. 1757683Myelin membrane adhesion molecule P0 [48728] (1 species)
  21. 1757686Myelin oligodendrocyte glycoprotein (MOG) [89174] (1 species)
  22. 1757693N-terminal domain of sialic acid binding Ig-like lectin 7 (SIGLEC-7, p75/AIRM1) [89176] (1 species)
  23. 1757701N-terminal domain of sialoadhesin [48732] (1 species)
  24. 1757711NK cell activating receptor NKP44 [89178] (1 species)
    a triggering partner in natural cytotoxicity
  25. 1757714Novel antigen receptor (against lysozyme) [110042] (1 species)
  26. 1757720Novel antigen receptor 12Y-1 [110044] (1 species)
  27. 1757723Novel antigen receptor 12Y-2 [110046] (1 species)
  28. 1757727Polymeric-immunoglobulin receptor, PIGR [117038] (1 species)
  29. 1757735Programmed cell death protein 1, PD1, extracellular domain [101510] (2 species)
    1. 1757736Species Human (Homo sapiens) [TaxId:9606] [256383] (2 PDB entries)
    2. 1757739Species Mouse (Mus musculus) [TaxId:10090] [101511] (5 PDB entries)
  30. 1757747T-cell antigen receptor [48933] (6 species)
    sequences may differ within each classified species
    1. 1757748Species Human (Homo sapiens), alpha-chain [TaxId:9606] [48935] (21 PDB entries)
    2. 1757775Species Human (Homo sapiens), beta-chain [TaxId:9606] [48937] (29 PDB entries)
    3. 1757828Species Human (Homo sapiens), delta-chain [TaxId:9606] [48938] (3 PDB entries)
    4. 1757837Species Human (Homo sapiens), gamma-chain [TaxId:9606] [63651] (3 PDB entries)
    5. 1757852Species Mouse (Mus musculus), alpha-chain [TaxId:10090] [48934] (21 PDB entries)
    6. 1757890Species Mouse (Mus musculus), beta-chain [TaxId:10090] [48936] (28 PDB entries)
  31. 1757934TREM-1 (triggering receptor expressed on myeloid cells 1) [101506] (2 species)
    1. 1757935Species Human (Homo sapiens) [TaxId:9606] [101507] (2 PDB entries)
      Uniprot Q9NP99 21-133
    2. 1757942Species Mouse (Mus musculus) [TaxId:10090] [117037] (1 PDB entry)
      Uniprot Q9JKE2 25-134
  32. 1757945Tyrosine-protein kinase receptor tyro3, N-terminal domain [101508] (1 species)
  33. 1757949automated matches [190119] (18 species)
    not a true protein
    1. 1757950Species Camel (Camelus dromedarius) [TaxId:9838] [187219] (25 PDB entries)
    2. 1757999Species Cow (Bos taurus) [TaxId:9913] [197337] (1 PDB entry)
    3. 1758001Species Dogfish (Squalus acanthias) [TaxId:7797] [226656] (2 PDB entries)
    4. 1758005Species Human (Homo sapiens) [TaxId:9606] [188740] (120 PDB entries)
    5. 1758305Species Human herpesvirus 1 [TaxId:10299] [256116] (1 PDB entry)
    6. 1758307Species Human herpesvirus 2 [TaxId:10313] [259821] (1 PDB entry)
    7. 1758310Species Human herpesvirus 2 [TaxId:10315] [256151] (1 PDB entry)
    8. 1758312Species Lepus curpaeums [TaxId:9980] [279011] (1 PDB entry)
    9. 1758317Species Llama (Lama glama) [TaxId:9844] [187485] (93 PDB entries)
    10. 1758503Species Llama glama [TaxId:9844] [236993] (1 PDB entry)
    11. 1758510Species Macaca mulatta [TaxId:9541] [188468] (1 PDB entry)
    12. 1758513Species Mouse (Mus musculus) [TaxId:10090] [186842] (133 PDB entries)
    13. 1758768Species Norway rat (Rattus norvegicus) [TaxId:10116] [187415] (7 PDB entries)
    14. 1758784Species Nurse shark (Ginglymostoma cirratum) [TaxId:7801] [187220] (4 PDB entries)
    15. 1758792Species Ornithorhynchus anatinus [TaxId:9258] [228732] (1 PDB entry)
    16. 1758794Species Rat (Rattus rattus) [TaxId:10117] [225551] (1 PDB entry)
    17. 1758797Species Spotted wobbegong (Orectolobus maculatus) [TaxId:168098] [187564] (5 PDB entries)
    18. 1758808Species Vicugna pacos [TaxId:30538] [189756] (9 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):