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

  1. Root: SCOPe 2.07
  2. 2352458Class b: All beta proteins [48724] (178 folds)
  3. 2352459Fold 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. 2352460Superfamily b.1.1: Immunoglobulin [48726] (5 families) (S)
  5. 2352461Family b.1.1.1: V set domains (antibody variable domain-like) [48727] (33 proteins)

Proteins:

  1. 2352462Alphaherpesvirus glycoprotein E [141008] (1 species)
    elaborated with insertions and C-terminal extensions
  2. 2352468B- and T-lymphocyte attenuator CD272 [158869] (1 species)
  3. 2352472Biliary glycoprotein C (CD66a, CEACAM1A[1,4]), N-terminal domain [81942] (1 species)
  4. 2352475Camelid IG heavy chain variable domain, VHh [88563] (3 species)
    1. 2352476Species Camel (Camelus dromedarius) [TaxId:9838] [88564] (19 PDB entries)
      SQ NA # camelid antibody
    2. 2352510Species Human (Homo sapiens) [TaxId:9606] [158863] (2 PDB entries)
    3. 2352515Species Llama (Lama glama) [TaxId:9844] [88565] (7 PDB entries)
  5. 2352524CD2, first domain [48740] (2 species)
    1. 2352525Species Human (Homo sapiens) [TaxId:9606] [48741] (4 PDB entries)
    2. 2352531Species Norway rat (Rattus norvegicus) [TaxId:10116] [48742] (5 PDB entries)
  6. 2352544CD2-binding domain of CD58, N-terminal domain [48743] (1 species)
  7. 2352550CD28 [158865] (1 species)
    T-cell-specific surface glycoprotein
  8. 2352553CD4 V-set domains [48737] (2 species)
    1. 2352554Species Human (Homo sapiens) [TaxId:9606] [48738] (33 PDB entries)
    2. 2352599Species Rat (Rattus rattus) [TaxId:10117] [48739] (1 PDB entry)
  9. 2352601CD8 [48734] (3 species)
    1. 2352602Species Human (Homo sapiens) [TaxId:9606] [48735] (3 PDB entries)
    2. 2352610Species Mouse (Mus musculus) [TaxId:10090] [48736] (5 PDB entries)
    3. 2352623Species Mouse (Mus musculus), beta-chain [TaxId:10090] [158864] (2 PDB entries)
      Uniprot P10300 22-136
  10. 2352628CD80, N-terminal domain [48745] (1 species)
    a soluble form of b7-1
  11. 2352633CD86 (b7-2), N-terminal domain [63635] (1 species)
  12. 2352643Coxsackie virus and adenovirus receptor (Car), domain 1 [48730] (1 species)
  13. 2352665HSV glycoprotein D [63637] (1 species)
  14. 2352672Immunoglobulin 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. 2352673Species Chinese hamster (Cricetulus griseus) [TaxId:10029] [88561] (1 PDB entry)
    2. 2352676Species Engineered (including hybrid species) [88562] (71 PDB entries)
      SQ NA # humanized antidoby; bactericidal Fab-h6831 ! SQ NA # humanized antibody ! SQ NA # Humanized antibody ! SQ NA # engineered antibody
    3. 2352784Species Escherichia coli [TaxId:316407] [343346] (1 PDB entry)
    4. 2352787Species Human (Homo sapiens), cluster 1 [TaxId:9606] [88544] (37 PDB entries)
    5. 2352848Species Human (Homo sapiens), cluster 2.1 [TaxId:9606] [88545] (3 PDB entries)
    6. 2352854Species Human (Homo sapiens), cluster 2.2 [TaxId:9606] [88546] (2 PDB entries)
    7. 2352857Species 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. 2352932Species Human (Homo sapiens), cluster 4 [TaxId:9606] [101505] (4 PDB entries)
    9. 2352940Species Mouse (Mus musculus), cluster 1 [TaxId:10090] [88548] (68 PDB entries)
      Uniprot P01796 # ! HV27_MOUSE Ig heavy chain V-III region A4
    10. 2353030Species 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. 2353053Species Mouse (Mus musculus), cluster 2.2 [TaxId:10090] [88550] (61 PDB entries)
      Uniprot P01811 # HV41_MOUSE (P01811) Ig heavy chain V region UPC10
    12. 2353147Species 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. 2353188Species 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. 2353422Species Mouse (Mus musculus), cluster 3.3 [TaxId:10090] [88553] (1 PDB entry)
    15. 2353425Species 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. 2353475Species Mouse (Mus musculus), cluster 5 [TaxId:10090] [88555] (36 PDB entries)
    17. 2353523Species Mouse (Mus musculus), cluster 6 [TaxId:10090] [88556] (12 PDB entries)
      SQ NA # part of Fab 28 against HIV-1 RT
    18. 2353538Species Mouse (Mus musculus), cluster 7.1 [TaxId:10090] [88557] (39 PDB entries)
      Uniprot P18532 # HV61_MOUSE Ig heavy chain V region 1B43 precursor
    19. 2353587Species Mouse (Mus musculus), cluster 7.2 [TaxId:10090] [88558] (32 PDB entries)
    20. 2353623Species Mouse (Mus musculus), cluster 7.3 [TaxId:10090] [88559] (2 PDB entries)
    21. 2353626Species Norway rat (Rattus norvegicus) [TaxId:10116] [88560] (16 PDB entries)
    22. 2353659Species Synthetic construct [TaxId:32630] [158862] (3 PDB entries)
  15. 2353665Immunoglobulin 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. 2353666Species Engineered (including hybrid species) [88533] (63 PDB entries)
      SQ NA # humanized antidoby; bactericidal Fab-h6831 ! SQ NA # Humanized antibody ! SQ NA # humanized antibody ! SQ NA # engineered antibody
    2. 2353751Species Escherichia coli [TaxId:562] [224853] (1 PDB entry)
    3. 2353753Species Human (Homo sapiens), cluster 1 [TaxId:9606] [88520] (19 PDB entries)
    4. 2353797Species Human (Homo sapiens), cluster 2 [TaxId:9606] [88521] (10 PDB entries)
    5. 2353813Species Human (Homo sapiens), cluster 3.1 [TaxId:9606] [88522] (8 PDB entries)
    6. 2353828Species Human (Homo sapiens), cluster 3.2 [TaxId:9606] [88523] (31 PDB entries)
    7. 2353891Species 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. 2354061Species Mouse (Mus musculus), cluster 1.2 [TaxId:10090] [88525] (51 PDB entries)
    9. 2354130Species Mouse (Mus musculus), cluster 2 [TaxId:10090] [88526] (28 PDB entries)
    10. 2354171Species Mouse (Mus musculus), cluster 3.1 [TaxId:10090] [88527] (13 PDB entries)
    11. 2354190Species 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. 2354262Species Mouse (Mus musculus), cluster 3.3 [TaxId:10090] [88529] (2 PDB entries)
    13. 2354266Species Mouse (Mus musculus), cluster 3.4 [TaxId:10090] [88530] (4 PDB entries)
    14. 2354271Species 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. 2354560Species Norway rat (Rattus norvegicus) [TaxId:10116] [88532] (14 PDB entries)
    16. 2354583Species Synthetic construct [TaxId:32630] [158859] (2 PDB entries)
  16. 2354589Immunoglobulin 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. 2354590Species Chinese hamster (Cricetulus griseus) [TaxId:10029] [88542] (1 PDB entry)
    2. 2354593Species 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. 2354602Species Human (Homo sapiens), cluster 2 [TaxId:9606] [88536] (10 PDB entries)
    4. 2354617Species Human (Homo sapiens), cluster 3.1 [TaxId:9606] [88537] (1 PDB entry)
    5. 2354619Species Human (Homo sapiens), cluster 3.2 [TaxId:9606] [88538] (1 PDB entry)
    6. 2354621Species Human (Homo sapiens), cluster 4 [TaxId:9606] [88539] (23 PDB entries)
    7. 2354667Species 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. 2354681Species Mouse (Mus musculus) [TaxId:10090] [88541] (36 PDB entries)
    9. 2354731Species Norway rat (Rattus norvegicus) [TaxId:10116] [101504] (7 PDB entries)
  17. 2354752Immunoreceptor CTLA-4 (CD152), N-terminal fragment [48939] (2 species)
    1. 2354753Species Human (Homo sapiens) [TaxId:9606] [48940] (8 PDB entries)
    2. 2354764Species Mouse (Mus musculus) [TaxId:10090] [48941] (3 PDB entries)
  18. 2354774Junction adhesion molecule, JAM, N-terminal domain [48747] (2 species)
    1. 2354775Species Human (Homo sapiens) [TaxId:9606] [89180] (1 PDB entry)
    2. 2354778Species Mouse (Mus musculus) [TaxId:10090] [48748] (1 PDB entry)
  19. 2354780Kin of IRRE-like protein 3, KIRREL3 [158867] (1 species)
  20. 2354783Myelin membrane adhesion molecule P0 [48728] (1 species)
  21. 2354786Myelin oligodendrocyte glycoprotein (MOG) [89174] (1 species)
  22. 2354793N-terminal domain of sialic acid binding Ig-like lectin 7 (SIGLEC-7, p75/AIRM1) [89176] (1 species)
  23. 2354801N-terminal domain of sialoadhesin [48732] (1 species)
  24. 2354811NK cell activating receptor NKP44 [89178] (1 species)
    a triggering partner in natural cytotoxicity
  25. 2354814Novel antigen receptor (against lysozyme) [110042] (1 species)
  26. 2354820Novel antigen receptor 12Y-1 [110044] (1 species)
  27. 2354823Novel antigen receptor 12Y-2 [110046] (1 species)
  28. 2354827Polymeric-immunoglobulin receptor, PIGR [117038] (1 species)
  29. 2354835Programmed cell death protein 1, PD1, extracellular domain [101510] (2 species)
    1. 2354836Species Human (Homo sapiens) [TaxId:9606] [256383] (9 PDB entries)
    2. 2354852Species Mouse (Mus musculus) [TaxId:10090] [101511] (7 PDB entries)
  30. 2354864T-cell antigen receptor [48933] (6 species)
    sequences may differ within each classified species
    1. 2354865Species Human (Homo sapiens), alpha-chain [TaxId:9606] [48935] (21 PDB entries)
    2. 2354892Species Human (Homo sapiens), beta-chain [TaxId:9606] [48937] (30 PDB entries)
    3. 2354946Species Human (Homo sapiens), delta-chain [TaxId:9606] [48938] (3 PDB entries)
    4. 2354955Species Human (Homo sapiens), gamma-chain [TaxId:9606] [63651] (3 PDB entries)
    5. 2354970Species Mouse (Mus musculus), alpha-chain [TaxId:10090] [48934] (22 PDB entries)
    6. 2355009Species Mouse (Mus musculus), beta-chain [TaxId:10090] [48936] (28 PDB entries)
  31. 2355053TREM-1 (triggering receptor expressed on myeloid cells 1) [101506] (2 species)
    1. 2355054Species Human (Homo sapiens) [TaxId:9606] [101507] (2 PDB entries)
      Uniprot Q9NP99 21-133
    2. 2355061Species Mouse (Mus musculus) [TaxId:10090] [117037] (1 PDB entry)
      Uniprot Q9JKE2 25-134
  32. 2355064Tyrosine-protein kinase receptor tyro3, N-terminal domain [101508] (1 species)
  33. 2355068automated matches [190119] (22 species)
    not a true protein
    1. 2355069Species Camel (Camelus dromedarius) [TaxId:9838] [187219] (42 PDB entries)
    2. 2355154Species Camelus bactrianus [TaxId:9837] [371849] (5 PDB entries)
    3. 2355164Species Cow (Bos taurus) [TaxId:9913] [197337] (3 PDB entries)
    4. 2355170Species Dogfish (Squalus acanthias) [TaxId:7797] [226656] (2 PDB entries)
    5. 2355174Species Escherichia coli [TaxId:83333] [354477] (2 PDB entries)
    6. 2355178Species Human (Homo sapiens) [TaxId:9606] [188740] (320 PDB entries)
    7. 2355824Species Human herpesvirus 1 [TaxId:10299] [256116] (1 PDB entry)
    8. 2355826Species Human herpesvirus 2 [TaxId:10313] [259821] (1 PDB entry)
    9. 2355829Species Human herpesvirus 2 [TaxId:10315] [256151] (1 PDB entry)
    10. 2355831Species Llama (Lama glama) [TaxId:9844] [187485] (223 PDB entries)
    11. 2356316Species Llama glama [TaxId:9844] [236993] (1 PDB entry)
    12. 2356323Species Macaca mulatta [TaxId:9541] [188468] (1 PDB entry)
    13. 2356326Species Macaca mulatta [TaxId:9544] [377132] (3 PDB entries)
    14. 2356330Species Mouse (Mus musculus) [TaxId:10090] [186842] (212 PDB entries)
    15. 2356727Species Norway rat (Rattus norvegicus) [TaxId:10116] [187415] (7 PDB entries)
    16. 2356743Species Nurse shark (Ginglymostoma cirratum) [TaxId:7801] [187220] (4 PDB entries)
    17. 2356751Species Ornithorhynchus anatinus [TaxId:9258] [228732] (1 PDB entry)
    18. 2356753Species Pig (Sus scrofa) [TaxId:9823] [322548] (1 PDB entry)
    19. 2356756Species Rabbit (Oryctolagus cuniculus) [TaxId:9986] [331472] (3 PDB entries)
    20. 2356764Species Rat (Rattus rattus) [TaxId:10117] [225551] (1 PDB entry)
    21. 2356767Species Spotted wobbegong (Orectolobus maculatus) [TaxId:168098] [187564] (9 PDB entries)
    22. 2356783Species Vicugna pacos [TaxId:30538] [189756] (79 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):