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

  1. Root: SCOP 1.75
  2. 781541Class b: All beta proteins [48724] (174 folds)
  3. 781542Fold b.1: Immunoglobulin-like beta-sandwich [48725] (28 superfamilies)
    sandwich; 7 strands in 2 sheets; greek-key
    some members of the fold have additional strands
  4. 781543Superfamily b.1.1: Immunoglobulin [48726] (4 families) (S)
  5. 781544Family b.1.1.1: V set domains (antibody variable domain-like) [48727] (32 proteins)

Proteins:

  1. 781545Alphaherpesvirus glycoprotein E [141008] (1 species)
    elaborated with insertions and C-terminal extensions
  2. 781551B- and T-lymphocyte attenuator CD272 [158869] (1 species)
  3. 781555Biliary glycoprotein C (CD66a, CEACAM1A[1,4]), N-terminal domain [81942] (1 species)
  4. 781558Camelid IG heavy chain variable domain, VHh [88563] (3 species)
    1. 781559Species Camel (Camelus dromedarius) [TaxId:9838] [88564] (22 PDB entries)
      SQ NA # camelid antibody
    2. 781597Species Homo sapiens [TaxId:9606] [158863] (1 PDB entry)
    3. 781600Species Llama (Lama glama) [TaxId:9844] [88565] (8 PDB entries)
  5. 781611CD2, first domain [48740] (2 species)
    1. 781612Species Human (Homo sapiens) [TaxId:9606] [48741] (4 PDB entries)
    2. 781618Species Rat (Rattus norvegicus) [TaxId:10116] [48742] (5 PDB entries)
  6. 781631CD2-binding domain of CD58, N-terminal domain [48743] (1 species)
  7. 781637CD28 [158865] (1 species)
    T-cell-specific surface glycoprotein
  8. 781640CD4 V-set domains [48737] (2 species)
    1. 781641Species Human (Homo sapiens) [TaxId:9606] [48738] (26 PDB entries)
    2. 781678Species Rat (Rattus rattus) [TaxId:10117] [48739] (1 PDB entry)
  9. 781680CD8 [48734] (3 species)
    1. 781681Species Human (Homo sapiens) [TaxId:9606] [48735] (2 PDB entries)
    2. 781685Species Mouse (Mus musculus) [TaxId:10090] [48736] (4 PDB entries)
    3. 781696Species Mouse (Mus musculus), beta-chain [TaxId:10090] [158864] (1 PDB entry)
      Uniprot P10300 22-136
  10. 781699CD80, N-terminal domain [48745] (1 species)
    a soluble form of b7-1
  11. 781704CD86 (b7-2), N-terminal domain [63635] (1 species)
  12. 781710Coxsackie virus and adenovirus receptor (Car), domain 1 [48730] (1 species)
  13. 781733HSV glycoprotein D [63637] (1 species)
  14. 781740Immunoglobulin 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. 781741Species 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
      SQ NA # humanized antidoby; bactericidal Fab-h6831 ! SQ NA # humanized antibody ! SQ NA # Humanized antibody ! SQ NA # engineered antibody
    2. 781843Species Escherichia coli [TaxId:562] [158861] (1 PDB entry)
    3. 781847Species Hamster (Cricetulus griseus) [TaxId:10029] [88561] (1 PDB entry)
    4. 781850Species Human (Homo sapiens), cluster 1 [TaxId:9606] [88544] (36 PDB entries)
    5. 781910Species Human (Homo sapiens), cluster 2.1 [TaxId:9606] [88545] (3 PDB entries)
    6. 781916Species Human (Homo sapiens), cluster 2.2 [TaxId:9606] [88546] (2 PDB entries)
    7. 781920Species 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)
    8. 781992Species Human (Homo sapiens), cluster 4 [TaxId:9606] [101505] (3 PDB entries)
    9. 781998Species Mouse (Mus musculus), cluster 1 [TaxId:10090] [88548] (47 PDB entries)
      Uniprot P01796 #
      HV27_MOUSE Ig heavy chain V-III region A4
      Uniprot P01796 # ! HV27_MOUSE Ig heavy chain V-III region A4
    10. 782061Species 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
    11. 782083Species Mouse (Mus musculus), cluster 2.2 [TaxId:10090] [88550] (54 PDB entries)
      Uniprot P01811 # HV41_MOUSE (P01811) Ig heavy chain V region UPC10
    12. 782163Species 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)
    13. 782204Species Mouse (Mus musculus), cluster 3.2 [TaxId:10090] [88552] (152 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
      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. 782406Species Mouse (Mus musculus), cluster 3.3 [TaxId:10090] [88553] (1 PDB entry)
    15. 782409Species Mouse (Mus musculus), cluster 4 [TaxId:10090] [88554] (32 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
      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. 782455Species Mouse (Mus musculus), cluster 5 [TaxId:10090] [88555] (36 PDB entries)
    17. 782503Species Mouse (Mus musculus), cluster 6 [TaxId:10090] [88556] (12 PDB entries)
      SQ NA # part of Fab 28 against HIV-1 RT
    18. 782518Species Mouse (Mus musculus), cluster 7.1 [TaxId:10090] [88557] (38 PDB entries)
      Uniprot P18532 # HV61_MOUSE Ig heavy chain V region 1B43 precursor
    19. 782566Species Mouse (Mus musculus), cluster 7.2 [TaxId:10090] [88558] (28 PDB entries)
    20. 782598Species Mouse (Mus musculus), cluster 7.3 [TaxId:10090] [88559] (2 PDB entries)
    21. 782601Species Rat (Rattus norvegicus) [TaxId:10116] [88560] (16 PDB entries)
    22. 782634Species synthetic construct [TaxId:32630] [158862] (2 PDB entries)
  15. 782637Immunoglobulin 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. 782638Species Engineered (including hybrid species) [88533] (52 PDB entries)
      SQ NA # humanized antidoby; bactericidal Fab-h6831
      SQ NA # Humanized antibody
      SQ NA # humanized antibody
      SQ NA # engineered antibody
      SQ NA # humanized antidoby; bactericidal Fab-h6831 ! SQ NA # Humanized antibody ! SQ NA # humanized antibody ! SQ NA # engineered antibody
    2. 782710Species Escherichia coli [TaxId:562] [158860] (3 PDB entries)
    3. 782719Species Human (Homo sapiens), cluster 1 [TaxId:9606] [88520] (18 PDB entries)
    4. 782762Species Human (Homo sapiens), cluster 2 [TaxId:9606] [88521] (10 PDB entries)
    5. 782778Species Human (Homo sapiens), cluster 3.1 [TaxId:9606] [88522] (8 PDB entries)
    6. 782793Species Human (Homo sapiens), cluster 3.2 [TaxId:9606] [88523] (35 PDB entries)
    7. 782864Species Mouse (Mus musculus), cluster 1.1 [TaxId:10090] [88524] (127 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
      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. 783027Species Mouse (Mus musculus), cluster 1.2 [TaxId:10090] [88525] (36 PDB entries)
    9. 783080Species Mouse (Mus musculus), cluster 2 [TaxId:10090] [88526] (30 PDB entries)
    10. 783123Species Mouse (Mus musculus), cluster 3.1 [TaxId:10090] [88527] (13 PDB entries)
    11. 783142Species Mouse (Mus musculus), cluster 3.2 [TaxId:10090] [88528] (44 PDB entries)
      Uniprot P04940 # KV6F_MOUSE IG KAPPA CHAIN V-VI REGION NQ2-17.4.1
    12. 783215Species Mouse (Mus musculus), cluster 3.3 [TaxId:10090] [88529] (2 PDB entries)
    13. 783219Species Mouse (Mus musculus), cluster 3.4 [TaxId:10090] [88530] (6 PDB entries)
    14. 783226Species Mouse (Mus musculus), cluster 4 [TaxId:10090] [88531] (182 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
      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. 783460Species Rat (Rattus norvegicus) [TaxId:10116] [88532] (9 PDB entries)
    16. 783478Species synthetic construct [TaxId:32630] [158859] (1 PDB entry)
  16. 783480Immunoglobulin 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. 783481Species Hamster (Cricetulus griseus) [TaxId:10029] [88542] (1 PDB entry)
    2. 783484Species 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
      SQ NA # Bence-Jones protein JTO ! Uniprot P06317 # Ig lambda chain V-VI region SUT
    3. 783493Species Human (Homo sapiens), cluster 2 [TaxId:9606] [88536] (10 PDB entries)
    4. 783509Species Human (Homo sapiens), cluster 3.1 [TaxId:9606] [88537] (2 PDB entries)
    5. 783513Species Human (Homo sapiens), cluster 3.2 [TaxId:9606] [88538] (1 PDB entry)
    6. 783515Species Human (Homo sapiens), cluster 4 [TaxId:9606] [88539] (23 PDB entries)
    7. 783561Species 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. 783574Species Mouse (Mus musculus) [TaxId:10090] [88541] (34 PDB entries)
    9. 783621Species Rat (Rattus norvegicus) [TaxId:10116] [101504] (8 PDB entries)
  17. 783643Immunoreceptor CTLA-4 (CD152), N-terminal fragment [48939] (2 species)
    1. 783644Species Human (Homo sapiens) [TaxId:9606] [48940] (3 PDB entries)
    2. 783650Species Mouse (Mus musculus) [TaxId:10090] [48941] (1 PDB entry)
  18. 783655Junction adhesion molecule, JAM, N-terminal domain [48747] (2 species)
    1. 783656Species Human (Homo sapiens) [TaxId:9606] [89180] (1 PDB entry)
    2. 783659Species Mouse (Mus musculus) [TaxId:10090] [48748] (1 PDB entry)
  19. 783661Kin of IRRE-like protein 3, KIRREL3 [158867] (1 species)
  20. 783664Myelin membrane adhesion molecule P0 [48728] (1 species)
  21. 783667Myelin oligodendrocyte glycoprotein (MOG) [89174] (1 species)
  22. 783673N-terminal domain of sialic acid binding Ig-like lectin 7 (SIGLEC-7, p75/AIRM1) [89176] (1 species)
  23. 783681N-terminal domain of sialoadhesin [48732] (1 species)
  24. 783693NK cell activating receptor NKP44 [89178] (1 species)
    a triggering partner in natural cytotoxicity
  25. 783696Novel antigen receptor (against lysozyme) [110042] (1 species)
  26. 783706Novel antigen receptor 12Y-1 [110044] (1 species)
  27. 783709Novel antigen receptor 12Y-2 [110046] (1 species)
  28. 783713Polymeric-immunoglobulin receptor, PIGR [117038] (1 species)
  29. 783721Programmed cell death protein 1, PD1, extracellular domain [101510] (1 species)
  30. 783727T-cell antigen receptor [48933] (6 species)
    sequences may differ within each classified species
    1. 783728Species Human (Homo sapiens), alpha-chain [TaxId:9606] [48935] (17 PDB entries)
    2. 783750Species Human (Homo sapiens), beta-chain [TaxId:9606] [48937] (30 PDB entries)
    3. 783804Species Human (Homo sapiens), delta-chain [TaxId:9606] [48938] (3 PDB entries)
    4. 783813Species Human (Homo sapiens), gamma-chain [TaxId:9606] [63651] (3 PDB entries)
    5. 783828Species Mouse (Mus musculus), alpha-chain [TaxId:10090] [48934] (21 PDB entries)
    6. 783866Species Mouse (Mus musculus), beta-chain [TaxId:10090] [48936] (27 PDB entries)
  31. 783914TREM-1 (triggering receptor expressed on myeloid cells 1) [101506] (2 species)
    1. 783915Species Human (Homo sapiens) [TaxId:9606] [101507] (2 PDB entries)
      Uniprot Q9NP99 21-133
    2. 783922Species Mouse (Mus musculus) [TaxId:10090] [117037] (1 PDB entry)
      Uniprot Q9JKE2 25-134
  32. 783925Tyrosine-protein kinase receptor tyro3, N-terminal domain [101508] (1 species)

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):