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

  1. Root: SCOPe 2.06
  2. 2021373Class b: All beta proteins [48724] (177 folds)
  3. 2021374Fold 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. 2021375Superfamily b.1.1: Immunoglobulin [48726] (5 families) (S)
  5. 2021376Family b.1.1.1: V set domains (antibody variable domain-like) [48727] (33 proteins)

Proteins:

  1. 2021377Alphaherpesvirus glycoprotein E [141008] (1 species)
    elaborated with insertions and C-terminal extensions
  2. 2021383B- and T-lymphocyte attenuator CD272 [158869] (1 species)
  3. 2021387Biliary glycoprotein C (CD66a, CEACAM1A[1,4]), N-terminal domain [81942] (1 species)
  4. 2021390Camelid IG heavy chain variable domain, VHh [88563] (3 species)
    1. 2021391Species Camel (Camelus dromedarius) [TaxId:9838] [88564] (19 PDB entries)
      SQ NA # camelid antibody
    2. 2021425Species Human (Homo sapiens) [TaxId:9606] [158863] (2 PDB entries)
    3. 2021430Species Llama (Lama glama) [TaxId:9844] [88565] (7 PDB entries)
  5. 2021439CD2, first domain [48740] (2 species)
    1. 2021440Species Human (Homo sapiens) [TaxId:9606] [48741] (4 PDB entries)
    2. 2021446Species Norway rat (Rattus norvegicus) [TaxId:10116] [48742] (5 PDB entries)
  6. 2021459CD2-binding domain of CD58, N-terminal domain [48743] (1 species)
  7. 2021465CD28 [158865] (1 species)
    T-cell-specific surface glycoprotein
  8. 2021468CD4 V-set domains [48737] (2 species)
    1. 2021469Species Human (Homo sapiens) [TaxId:9606] [48738] (32 PDB entries)
    2. 2021513Species Rat (Rattus rattus) [TaxId:10117] [48739] (1 PDB entry)
  9. 2021515CD8 [48734] (3 species)
    1. 2021516Species Human (Homo sapiens) [TaxId:9606] [48735] (3 PDB entries)
    2. 2021524Species Mouse (Mus musculus) [TaxId:10090] [48736] (5 PDB entries)
    3. 2021537Species Mouse (Mus musculus), beta-chain [TaxId:10090] [158864] (2 PDB entries)
      Uniprot P10300 22-136
  10. 2021542CD80, N-terminal domain [48745] (1 species)
    a soluble form of b7-1
  11. 2021547CD86 (b7-2), N-terminal domain [63635] (1 species)
  12. 2021553Coxsackie virus and adenovirus receptor (Car), domain 1 [48730] (1 species)
  13. 2021575HSV glycoprotein D [63637] (1 species)
  14. 2021582Immunoglobulin 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. 2021583Species Chinese hamster (Cricetulus griseus) [TaxId:10029] [88561] (1 PDB entry)
    2. 2021586Species 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. 2021689Species Escherichia coli [TaxId:316407] [343346] (1 PDB entry)
    4. 2021692Species Human (Homo sapiens), cluster 1 [TaxId:9606] [88544] (37 PDB entries)
    5. 2021753Species Human (Homo sapiens), cluster 2.1 [TaxId:9606] [88545] (3 PDB entries)
    6. 2021759Species Human (Homo sapiens), cluster 2.2 [TaxId:9606] [88546] (2 PDB entries)
    7. 2021762Species 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. 2021834Species Human (Homo sapiens), cluster 4 [TaxId:9606] [101505] (4 PDB entries)
    9. 2021842Species Mouse (Mus musculus), cluster 1 [TaxId:10090] [88548] (68 PDB entries)
      Uniprot P01796 # ! HV27_MOUSE Ig heavy chain V-III region A4
    10. 2021932Species 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. 2021955Species Mouse (Mus musculus), cluster 2.2 [TaxId:10090] [88550] (59 PDB entries)
      Uniprot P01811 # HV41_MOUSE (P01811) Ig heavy chain V region UPC10
    12. 2022045Species 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. 2022086Species 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. 2022320Species Mouse (Mus musculus), cluster 3.3 [TaxId:10090] [88553] (1 PDB entry)
    15. 2022323Species 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. 2022373Species Mouse (Mus musculus), cluster 5 [TaxId:10090] [88555] (36 PDB entries)
    17. 2022421Species Mouse (Mus musculus), cluster 6 [TaxId:10090] [88556] (12 PDB entries)
      SQ NA # part of Fab 28 against HIV-1 RT
    18. 2022436Species Mouse (Mus musculus), cluster 7.1 [TaxId:10090] [88557] (39 PDB entries)
      Uniprot P18532 # HV61_MOUSE Ig heavy chain V region 1B43 precursor
    19. 2022485Species Mouse (Mus musculus), cluster 7.2 [TaxId:10090] [88558] (32 PDB entries)
    20. 2022521Species Mouse (Mus musculus), cluster 7.3 [TaxId:10090] [88559] (2 PDB entries)
    21. 2022524Species Norway rat (Rattus norvegicus) [TaxId:10116] [88560] (16 PDB entries)
    22. 2022557Species Synthetic construct [TaxId:32630] [158862] (3 PDB entries)
  15. 2022563Immunoglobulin 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. 2022564Species 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. 2022646Species Escherichia coli [TaxId:562] [224853] (1 PDB entry)
    3. 2022648Species Human (Homo sapiens), cluster 1 [TaxId:9606] [88520] (19 PDB entries)
    4. 2022692Species Human (Homo sapiens), cluster 2 [TaxId:9606] [88521] (10 PDB entries)
    5. 2022708Species Human (Homo sapiens), cluster 3.1 [TaxId:9606] [88522] (8 PDB entries)
    6. 2022723Species Human (Homo sapiens), cluster 3.2 [TaxId:9606] [88523] (31 PDB entries)
    7. 2022786Species 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. 2022956Species Mouse (Mus musculus), cluster 1.2 [TaxId:10090] [88525] (51 PDB entries)
    9. 2023025Species Mouse (Mus musculus), cluster 2 [TaxId:10090] [88526] (28 PDB entries)
    10. 2023066Species Mouse (Mus musculus), cluster 3.1 [TaxId:10090] [88527] (13 PDB entries)
    11. 2023085Species 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. 2023153Species Mouse (Mus musculus), cluster 3.3 [TaxId:10090] [88529] (2 PDB entries)
    13. 2023157Species Mouse (Mus musculus), cluster 3.4 [TaxId:10090] [88530] (4 PDB entries)
    14. 2023162Species Mouse (Mus musculus), cluster 4 [TaxId:10090] [88531] (220 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. 2023437Species Norway rat (Rattus norvegicus) [TaxId:10116] [88532] (9 PDB entries)
    16. 2023455Species Synthetic construct [TaxId:32630] [158859] (2 PDB entries)
  16. 2023461Immunoglobulin 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. 2023462Species Chinese hamster (Cricetulus griseus) [TaxId:10029] [88542] (1 PDB entry)
    2. 2023465Species 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. 2023474Species Human (Homo sapiens), cluster 2 [TaxId:9606] [88536] (10 PDB entries)
    4. 2023489Species Human (Homo sapiens), cluster 3.1 [TaxId:9606] [88537] (1 PDB entry)
    5. 2023491Species Human (Homo sapiens), cluster 3.2 [TaxId:9606] [88538] (1 PDB entry)
    6. 2023493Species Human (Homo sapiens), cluster 4 [TaxId:9606] [88539] (23 PDB entries)
    7. 2023539Species 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. 2023552Species Mouse (Mus musculus) [TaxId:10090] [88541] (35 PDB entries)
    9. 2023600Species Norway rat (Rattus norvegicus) [TaxId:10116] [101504] (7 PDB entries)
  17. 2023621Immunoreceptor CTLA-4 (CD152), N-terminal fragment [48939] (2 species)
    1. 2023622Species Human (Homo sapiens) [TaxId:9606] [48940] (4 PDB entries)
    2. 2023629Species Mouse (Mus musculus) [TaxId:10090] [48941] (3 PDB entries)
  18. 2023639Junction adhesion molecule, JAM, N-terminal domain [48747] (2 species)
    1. 2023640Species Human (Homo sapiens) [TaxId:9606] [89180] (1 PDB entry)
    2. 2023643Species Mouse (Mus musculus) [TaxId:10090] [48748] (1 PDB entry)
  19. 2023645Kin of IRRE-like protein 3, KIRREL3 [158867] (1 species)
  20. 2023648Myelin membrane adhesion molecule P0 [48728] (1 species)
  21. 2023651Myelin oligodendrocyte glycoprotein (MOG) [89174] (1 species)
  22. 2023658N-terminal domain of sialic acid binding Ig-like lectin 7 (SIGLEC-7, p75/AIRM1) [89176] (1 species)
  23. 2023666N-terminal domain of sialoadhesin [48732] (1 species)
  24. 2023676NK cell activating receptor NKP44 [89178] (1 species)
    a triggering partner in natural cytotoxicity
  25. 2023679Novel antigen receptor (against lysozyme) [110042] (1 species)
  26. 2023685Novel antigen receptor 12Y-1 [110044] (1 species)
  27. 2023688Novel antigen receptor 12Y-2 [110046] (1 species)
  28. 2023692Polymeric-immunoglobulin receptor, PIGR [117038] (1 species)
  29. 2023700Programmed cell death protein 1, PD1, extracellular domain [101510] (2 species)
    1. 2023701Species Human (Homo sapiens) [TaxId:9606] [256383] (3 PDB entries)
    2. 2023706Species Mouse (Mus musculus) [TaxId:10090] [101511] (6 PDB entries)
  30. 2023718T-cell antigen receptor [48933] (6 species)
    sequences may differ within each classified species
    1. 2023719Species Human (Homo sapiens), alpha-chain [TaxId:9606] [48935] (21 PDB entries)
    2. 2023746Species Human (Homo sapiens), beta-chain [TaxId:9606] [48937] (29 PDB entries)
    3. 2023799Species Human (Homo sapiens), delta-chain [TaxId:9606] [48938] (3 PDB entries)
    4. 2023808Species Human (Homo sapiens), gamma-chain [TaxId:9606] [63651] (3 PDB entries)
    5. 2023823Species Mouse (Mus musculus), alpha-chain [TaxId:10090] [48934] (22 PDB entries)
    6. 2023862Species Mouse (Mus musculus), beta-chain [TaxId:10090] [48936] (28 PDB entries)
  31. 2023906TREM-1 (triggering receptor expressed on myeloid cells 1) [101506] (2 species)
    1. 2023907Species Human (Homo sapiens) [TaxId:9606] [101507] (2 PDB entries)
      Uniprot Q9NP99 21-133
    2. 2023914Species Mouse (Mus musculus) [TaxId:10090] [117037] (1 PDB entry)
      Uniprot Q9JKE2 25-134
  32. 2023917Tyrosine-protein kinase receptor tyro3, N-terminal domain [101508] (1 species)
  33. 2023921automated matches [190119] (22 species)
    not a true protein
    1. 2023922Species Camel (Camelus dromedarius) [TaxId:9838] [187219] (33 PDB entries)
    2. 2023989Species Cow (Bos taurus) [TaxId:9913] [197337] (2 PDB entries)
    3. 2023993Species Dogfish (Squalus acanthias) [TaxId:7797] [226656] (2 PDB entries)
    4. 2023997Species Escherichia coli [TaxId:562] [336108] (1 PDB entry)
    5. 2023999Species Helicobacter pylori [TaxId:210] [314169] (1 PDB entry)
    6. 2024002Species Human (Homo sapiens) [TaxId:9606] [188740] (183 PDB entries)
    7. 2024413Species Human herpesvirus 1 [TaxId:10299] [256116] (1 PDB entry)
    8. 2024415Species Human herpesvirus 2 [TaxId:10313] [259821] (1 PDB entry)
    9. 2024418Species Human herpesvirus 2 [TaxId:10315] [256151] (1 PDB entry)
    10. 2024420Species Lepus curpaeums [TaxId:9980] [279011] (1 PDB entry)
    11. 2024425Species Llama (Lama glama) [TaxId:9844] [187485] (138 PDB entries)
    12. 2024723Species Llama glama [TaxId:9844] [236993] (1 PDB entry)
    13. 2024730Species Macaca mulatta [TaxId:9541] [188468] (1 PDB entry)
    14. 2024733Species Mouse (Mus musculus) [TaxId:10090] [186842] (156 PDB entries)
    15. 2025022Species Norway rat (Rattus norvegicus) [TaxId:10116] [187415] (7 PDB entries)
    16. 2025038Species Nurse shark (Ginglymostoma cirratum) [TaxId:7801] [187220] (4 PDB entries)
    17. 2025046Species Ornithorhynchus anatinus [TaxId:9258] [228732] (1 PDB entry)
    18. 2025048Species Oryctolagus cuniculus [TaxId:9986] [331472] (1 PDB entry)
    19. 2025050Species Rat (Rattus rattus) [TaxId:10117] [225551] (1 PDB entry)
    20. 2025053Species Spotted wobbegong (Orectolobus maculatus) [TaxId:168098] [187564] (8 PDB entries)
    21. 2025067Species Sus scrofa [TaxId:9823] [322548] (1 PDB entry)
    22. 2025070Species Vicugna pacos [TaxId:30538] [189756] (35 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):