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

  1. Root: SCOPe 2.07
  2. 2344607Class b: All beta proteins [48724] (178 folds)
  3. 2344608Fold 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. 2344609Superfamily b.1.1: Immunoglobulin [48726] (5 families) (S)
  5. 2344610Family b.1.1.1: V set domains (antibody variable domain-like) [48727] (33 protein domains)

Protein Domains:

  1. 2344611Alphaherpesvirus glycoprotein E [141008] (1 species)
    elaborated with insertions and C-terminal extensions
  2. 2344617B- and T-lymphocyte attenuator CD272 [158869] (1 species)
  3. 2344621Biliary glycoprotein C (CD66a, CEACAM1A[1,4]), N-terminal domain [81942] (1 species)
  4. 2344624Camelid IG heavy chain variable domain, VHh [88563] (3 species)
    1. 2344625Species Camel (Camelus dromedarius) [TaxId:9838] [88564] (19 PDB entries)
      SQ NA # camelid antibody
    2. 2344659Species Human (Homo sapiens) [TaxId:9606] [158863] (2 PDB entries)
    3. 2344664Species Llama (Lama glama) [TaxId:9844] [88565] (7 PDB entries)
  5. 2344673CD2, first domain [48740] (2 species)
    1. 2344674Species Human (Homo sapiens) [TaxId:9606] [48741] (4 PDB entries)
    2. 2344680Species Norway rat (Rattus norvegicus) [TaxId:10116] [48742] (5 PDB entries)
  6. 2344693CD2-binding domain of CD58, N-terminal domain [48743] (1 species)
  7. 2344699CD28 [158865] (1 species)
    T-cell-specific surface glycoprotein
  8. 2344702CD4 V-set domains [48737] (2 species)
    1. 2344703Species Human (Homo sapiens) [TaxId:9606] [48738] (32 PDB entries)
    2. 2344747Species Rat (Rattus rattus) [TaxId:10117] [48739] (1 PDB entry)
  9. 2344749CD8 [48734] (3 species)
    1. 2344750Species Human (Homo sapiens) [TaxId:9606] [48735] (3 PDB entries)
    2. 2344758Species Mouse (Mus musculus) [TaxId:10090] [48736] (5 PDB entries)
    3. 2344771Species Mouse (Mus musculus), beta-chain [TaxId:10090] [158864] (2 PDB entries)
      Uniprot P10300 22-136
  10. 2344776CD80, N-terminal domain [48745] (1 species)
    a soluble form of b7-1
  11. 2344781CD86 (b7-2), N-terminal domain [63635] (1 species)
  12. 2344787Coxsackie virus and adenovirus receptor (Car), domain 1 [48730] (1 species)
  13. 2344809HSV glycoprotein D [63637] (1 species)
  14. 2344816Immunoglobulin 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. 2344817Species Chinese hamster (Cricetulus griseus) [TaxId:10029] [88561] (1 PDB entry)
    2. 2344820Species 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. 2344923Species Escherichia coli [TaxId:316407] [343346] (1 PDB entry)
    4. 2344926Species Human (Homo sapiens), cluster 1 [TaxId:9606] [88544] (37 PDB entries)
    5. 2344987Species Human (Homo sapiens), cluster 2.1 [TaxId:9606] [88545] (3 PDB entries)
    6. 2344993Species Human (Homo sapiens), cluster 2.2 [TaxId:9606] [88546] (2 PDB entries)
    7. 2344996Species Human (Homo sapiens), cluster 3 [TaxId:9606] [88547] (35 PDB entries)
      Uniprot Q6N089 20-243 # 95% sequence identity; natural chimera: antibody heavy chain (Fab HYB3)
    8. 2345071Species Human (Homo sapiens), cluster 4 [TaxId:9606] [101505] (4 PDB entries)
    9. 2345079Species Mouse (Mus musculus), cluster 1 [TaxId:10090] [88548] (68 PDB entries)
      Uniprot P01796 # ! HV27_MOUSE Ig heavy chain V-III region A4
    10. 2345169Species 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. 2345192Species Mouse (Mus musculus), cluster 2.2 [TaxId:10090] [88550] (59 PDB entries)
      Uniprot P01811 # HV41_MOUSE (P01811) Ig heavy chain V region UPC10
    12. 2345282Species 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. 2345323Species Mouse (Mus musculus), cluster 3.2 [TaxId:10090] [88552] (184 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. 2345557Species Mouse (Mus musculus), cluster 3.3 [TaxId:10090] [88553] (1 PDB entry)
    15. 2345560Species 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. 2345610Species Mouse (Mus musculus), cluster 5 [TaxId:10090] [88555] (36 PDB entries)
    17. 2345658Species Mouse (Mus musculus), cluster 6 [TaxId:10090] [88556] (12 PDB entries)
      SQ NA # part of Fab 28 against HIV-1 RT
    18. 2345673Species Mouse (Mus musculus), cluster 7.1 [TaxId:10090] [88557] (39 PDB entries)
      Uniprot P18532 # HV61_MOUSE Ig heavy chain V region 1B43 precursor
    19. 2345722Species Mouse (Mus musculus), cluster 7.2 [TaxId:10090] [88558] (32 PDB entries)
    20. 2345758Species Mouse (Mus musculus), cluster 7.3 [TaxId:10090] [88559] (2 PDB entries)
    21. 2345761Species Norway rat (Rattus norvegicus) [TaxId:10116] [88560] (16 PDB entries)
    22. 2345794Species Synthetic construct [TaxId:32630] [158862] (3 PDB entries)
  15. 2345800Immunoglobulin 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. 2345801Species 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. 2345883Species Escherichia coli [TaxId:562] [224853] (1 PDB entry)
    3. 2345885Species Human (Homo sapiens), cluster 1 [TaxId:9606] [88520] (19 PDB entries)
    4. 2345929Species Human (Homo sapiens), cluster 2 [TaxId:9606] [88521] (10 PDB entries)
    5. 2345945Species Human (Homo sapiens), cluster 3.1 [TaxId:9606] [88522] (8 PDB entries)
    6. 2345960Species Human (Homo sapiens), cluster 3.2 [TaxId:9606] [88523] (31 PDB entries)
    7. 2346023Species 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. 2346193Species Mouse (Mus musculus), cluster 1.2 [TaxId:10090] [88525] (51 PDB entries)
    9. 2346262Species Mouse (Mus musculus), cluster 2 [TaxId:10090] [88526] (28 PDB entries)
    10. 2346303Species Mouse (Mus musculus), cluster 3.1 [TaxId:10090] [88527] (13 PDB entries)
    11. 2346322Species 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. 2346390Species Mouse (Mus musculus), cluster 3.3 [TaxId:10090] [88529] (2 PDB entries)
    13. 2346394Species Mouse (Mus musculus), cluster 3.4 [TaxId:10090] [88530] (4 PDB entries)
    14. 2346399Species Mouse (Mus musculus), cluster 4 [TaxId:10090] [88531] (225 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. 2346679Species Norway rat (Rattus norvegicus) [TaxId:10116] [88532] (9 PDB entries)
    16. 2346697Species Synthetic construct [TaxId:32630] [158859] (2 PDB entries)
  16. 2346703Immunoglobulin 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. 2346704Species Chinese hamster (Cricetulus griseus) [TaxId:10029] [88542] (1 PDB entry)
    2. 2346707Species 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. 2346716Species Human (Homo sapiens), cluster 2 [TaxId:9606] [88536] (10 PDB entries)
    4. 2346731Species Human (Homo sapiens), cluster 3.1 [TaxId:9606] [88537] (1 PDB entry)
    5. 2346733Species Human (Homo sapiens), cluster 3.2 [TaxId:9606] [88538] (1 PDB entry)
    6. 2346735Species Human (Homo sapiens), cluster 4 [TaxId:9606] [88539] (23 PDB entries)
    7. 2346781Species 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. 2346795Species Mouse (Mus musculus) [TaxId:10090] [88541] (35 PDB entries)
    9. 2346843Species Norway rat (Rattus norvegicus) [TaxId:10116] [101504] (7 PDB entries)
  17. 2346864Immunoreceptor CTLA-4 (CD152), N-terminal fragment [48939] (2 species)
    1. 2346865Species Human (Homo sapiens) [TaxId:9606] [48940] (5 PDB entries)
    2. 2346873Species Mouse (Mus musculus) [TaxId:10090] [48941] (3 PDB entries)
  18. 2346883Junction adhesion molecule, JAM, N-terminal domain [48747] (2 species)
    1. 2346884Species Human (Homo sapiens) [TaxId:9606] [89180] (1 PDB entry)
    2. 2346887Species Mouse (Mus musculus) [TaxId:10090] [48748] (1 PDB entry)
  19. 2346889Kin of IRRE-like protein 3, KIRREL3 [158867] (1 species)
  20. 2346892Myelin membrane adhesion molecule P0 [48728] (1 species)
  21. 2346895Myelin oligodendrocyte glycoprotein (MOG) [89174] (1 species)
  22. 2346902N-terminal domain of sialic acid binding Ig-like lectin 7 (SIGLEC-7, p75/AIRM1) [89176] (1 species)
  23. 2346910N-terminal domain of sialoadhesin [48732] (1 species)
  24. 2346920NK cell activating receptor NKP44 [89178] (1 species)
    a triggering partner in natural cytotoxicity
  25. 2346923Novel antigen receptor (against lysozyme) [110042] (1 species)
  26. 2346929Novel antigen receptor 12Y-1 [110044] (1 species)
  27. 2346932Novel antigen receptor 12Y-2 [110046] (1 species)
  28. 2346936Polymeric-immunoglobulin receptor, PIGR [117038] (1 species)
  29. 2346944Programmed cell death protein 1, PD1, extracellular domain [101510] (2 species)
    1. 2346945Species Human (Homo sapiens) [TaxId:9606] [256383] (6 PDB entries)
    2. 2346957Species Mouse (Mus musculus) [TaxId:10090] [101511] (5 PDB entries)
  30. 2346965T-cell antigen receptor [48933] (6 species)
    sequences may differ within each classified species
    1. 2346966Species Human (Homo sapiens), alpha-chain [TaxId:9606] [48935] (21 PDB entries)
    2. 2346993Species Human (Homo sapiens), beta-chain [TaxId:9606] [48937] (29 PDB entries)
    3. 2347046Species Human (Homo sapiens), delta-chain [TaxId:9606] [48938] (3 PDB entries)
    4. 2347055Species Human (Homo sapiens), gamma-chain [TaxId:9606] [63651] (3 PDB entries)
    5. 2347070Species Mouse (Mus musculus), alpha-chain [TaxId:10090] [48934] (22 PDB entries)
    6. 2347109Species Mouse (Mus musculus), beta-chain [TaxId:10090] [48936] (28 PDB entries)
  31. 2347153TREM-1 (triggering receptor expressed on myeloid cells 1) [101506] (2 species)
    1. 2347154Species Human (Homo sapiens) [TaxId:9606] [101507] (2 PDB entries)
      Uniprot Q9NP99 21-133
    2. 2347161Species Mouse (Mus musculus) [TaxId:10090] [117037] (1 PDB entry)
      Uniprot Q9JKE2 25-134
  32. 2347164Tyrosine-protein kinase receptor tyro3, N-terminal domain [101508] (1 species)
  33. 2347168automated matches [190119] (20 species)
    not a true protein
    1. 2347169Species Camel (Camelus dromedarius) [TaxId:9838] [187219] (33 PDB entries)
    2. 2347236Species Cow (Bos taurus) [TaxId:9913] [197337] (2 PDB entries)
    3. 2347240Species Dogfish (Squalus acanthias) [TaxId:7797] [226656] (2 PDB entries)
    4. 2347244Species Human (Homo sapiens) [TaxId:9606] [188740] (193 PDB entries)
    5. 2347644Species Human herpesvirus 1 [TaxId:10299] [256116] (1 PDB entry)
    6. 2347646Species Human herpesvirus 2 [TaxId:10313] [259821] (1 PDB entry)
    7. 2347649Species Human herpesvirus 2 [TaxId:10315] [256151] (1 PDB entry)
    8. 2347651Species Llama (Lama glama) [TaxId:9844] [187485] (149 PDB entries)
    9. 2347941Species Llama glama [TaxId:9844] [236993] (1 PDB entry)
    10. 2347948Species Macaca mulatta [TaxId:9541] [188468] (1 PDB entry)
    11. 2347951Species Mouse (Mus musculus) [TaxId:10090] [186842] (160 PDB entries)
    12. 2348238Species Norway rat (Rattus norvegicus) [TaxId:10116] [187415] (7 PDB entries)
    13. 2348254Species Nurse shark (Ginglymostoma cirratum) [TaxId:7801] [187220] (4 PDB entries)
    14. 2348262Species Ornithorhynchus anatinus [TaxId:9258] [228732] (1 PDB entry)
    15. 2348264Species Pig (Sus scrofa) [TaxId:9823] [322548] (1 PDB entry)
    16. 2348267Species Rabbit (Oryctolagus cuniculus) [TaxId:9986] [331472] (2 PDB entries)
    17. 2348273Species Rat (Rattus rattus) [TaxId:10117] [225551] (1 PDB entry)
    18. 2348276Species Spotted wobbegong (Orectolobus maculatus) [TaxId:168098] [187564] (8 PDB entries)
    19. 2348290Species Vicugna pacos [TaxId:30538] [189756] (42 PDB entries)
    20. 3054415Species Escherichia coli [TaxId:83333] [354477] (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):