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

  1. Root: SCOPe 2.08
  2. 2739516Class b: All beta proteins [48724] (180 folds)
  3. 2739517Fold 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. 2739518Superfamily b.1.1: Immunoglobulin [48726] (5 families) (S)
  5. 2739519Family b.1.1.1: V set domains (antibody variable domain-like) [48727] (33 proteins)

Proteins:

  1. 2739520Alphaherpesvirus glycoprotein E [141008] (1 species)
    elaborated with insertions and C-terminal extensions
  2. 2739526B- and T-lymphocyte attenuator CD272 [158869] (1 species)
  3. 2739530Biliary glycoprotein C (CD66a, CEACAM1A[1,4]), N-terminal domain [81942] (1 species)
  4. 2739533Camelid IG heavy chain variable domain, VHh [88563] (3 species)
    1. 2739534Species Camel (Camelus dromedarius) [TaxId:9838] [88564] (19 PDB entries)
      SQ NA # camelid antibody
    2. 2739568Species Human (Homo sapiens) [TaxId:9606] [158863] (2 PDB entries)
    3. 2739573Species Llama (Lama glama) [TaxId:9844] [88565] (7 PDB entries)
  5. 2739582CD2, first domain [48740] (2 species)
    1. 2739583Species Human (Homo sapiens) [TaxId:9606] [48741] (4 PDB entries)
    2. 2739589Species Norway rat (Rattus norvegicus) [TaxId:10116] [48742] (5 PDB entries)
  6. 2739602CD2-binding domain of CD58, N-terminal domain [48743] (1 species)
  7. 2739608CD28 [158865] (1 species)
    T-cell-specific surface glycoprotein
  8. 2739611CD4 V-set domains [48737] (2 species)
    1. 2739612Species Human (Homo sapiens) [TaxId:9606] [48738] (33 PDB entries)
    2. 2739657Species Rat (Rattus rattus) [TaxId:10117] [48739] (1 PDB entry)
  9. 2739659CD8 [48734] (3 species)
    1. 2739660Species Human (Homo sapiens) [TaxId:9606] [48735] (3 PDB entries)
    2. 2739668Species Mouse (Mus musculus) [TaxId:10090] [48736] (5 PDB entries)
    3. 2739681Species Mouse (Mus musculus), beta-chain [TaxId:10090] [158864] (2 PDB entries)
      Uniprot P10300 22-136
  10. 2739686CD80, N-terminal domain [48745] (1 species)
    a soluble form of b7-1
  11. 2739691CD86 (b7-2), N-terminal domain [63635] (1 species)
  12. 2739701Coxsackie virus and adenovirus receptor (Car), domain 1 [48730] (1 species)
  13. 2739723HSV glycoprotein D [63637] (1 species)
  14. 2739730Immunoglobulin 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. 2739731Species Chinese hamster (Cricetulus griseus) [TaxId:10029] [88561] (1 PDB entry)
    2. 2739734Species 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
    3. 2739826Species Escherichia coli [TaxId:316407] [343346] (1 PDB entry)
    4. 2739829Species Human (Homo sapiens), cluster 1 [TaxId:9606] [88544] (37 PDB entries)
    5. 2739890Species Human (Homo sapiens), cluster 2.1 [TaxId:9606] [88545] (3 PDB entries)
    6. 2739896Species Human (Homo sapiens), cluster 2.2 [TaxId:9606] [88546] (2 PDB entries)
    7. 2739899Species Human (Homo sapiens), cluster 3 [TaxId:9606] [88547] (30 PDB entries)
      Uniprot Q6N089 20-243 # 95% sequence identity; natural chimera: antibody heavy chain (Fab HYB3)
    8. 2739966Species Human (Homo sapiens), cluster 4 [TaxId:9606] [101505] (4 PDB entries)
    9. 2739974Species Mouse (Mus musculus), cluster 1 [TaxId:10090] [88548] (68 PDB entries)
      Uniprot P01796 # ! HV27_MOUSE Ig heavy chain V-III region A4
    10. 2740064Species 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. 2740087Species Mouse (Mus musculus), cluster 2.2 [TaxId:10090] [88550] (62 PDB entries)
      Uniprot P01811 # HV41_MOUSE (P01811) Ig heavy chain V region UPC10
    12. 2740181Species Mouse (Mus musculus), cluster 3.1 [TaxId:10090] [88551] (30 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. 2740220Species Mouse (Mus musculus), cluster 3.2 [TaxId:10090] [88552] (181 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. 2740451Species Mouse (Mus musculus), cluster 3.3 [TaxId:10090] [88553] (1 PDB entry)
    15. 2740454Species 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. 2740504Species Mouse (Mus musculus), cluster 5 [TaxId:10090] [88555] (36 PDB entries)
    17. 2740552Species Mouse (Mus musculus), cluster 6 [TaxId:10090] [88556] (12 PDB entries)
      SQ NA # part of Fab 28 against HIV-1 RT
    18. 2740567Species Mouse (Mus musculus), cluster 7.1 [TaxId:10090] [88557] (40 PDB entries)
      Uniprot P18532 # HV61_MOUSE Ig heavy chain V region 1B43 precursor
    19. 2740618Species Mouse (Mus musculus), cluster 7.2 [TaxId:10090] [88558] (32 PDB entries)
    20. 2740654Species Mouse (Mus musculus), cluster 7.3 [TaxId:10090] [88559] (2 PDB entries)
    21. 2740657Species Norway rat (Rattus norvegicus) [TaxId:10116] [88560] (16 PDB entries)
    22. 2740690Species Synthetic construct [TaxId:32630] [158862] (3 PDB entries)
  15. 2740696Immunoglobulin 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. 2740697Species Engineered (including hybrid species) [88533] (60 PDB entries)
      SQ NA # humanized antidoby; bactericidal Fab-h6831 ! SQ NA # Humanized antibody ! SQ NA # humanized antibody ! SQ NA # engineered antibody
    2. 2740776Species Escherichia coli [TaxId:562] [224853] (1 PDB entry)
    3. 2740778Species Human (Homo sapiens), cluster 1 [TaxId:9606] [88520] (19 PDB entries)
    4. 2740822Species Human (Homo sapiens), cluster 2 [TaxId:9606] [88521] (10 PDB entries)
    5. 2740838Species Human (Homo sapiens), cluster 3.1 [TaxId:9606] [88522] (8 PDB entries)
    6. 2740853Species Human (Homo sapiens), cluster 3.2 [TaxId:9606] [88523] (31 PDB entries)
    7. 2740916Species 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. 2741086Species Mouse (Mus musculus), cluster 1.2 [TaxId:10090] [88525] (52 PDB entries)
    9. 2741155Species Mouse (Mus musculus), cluster 2 [TaxId:10090] [88526] (28 PDB entries)
    10. 2741196Species Mouse (Mus musculus), cluster 3.1 [TaxId:10090] [88527] (13 PDB entries)
    11. 2741215Species Mouse (Mus musculus), cluster 3.2 [TaxId:10090] [88528] (43 PDB entries)
      Uniprot P04940 # KV6F_MOUSE IG KAPPA CHAIN V-VI REGION NQ2-17.4.1
    12. 2741287Species Mouse (Mus musculus), cluster 3.3 [TaxId:10090] [88529] (2 PDB entries)
    13. 2741291Species Mouse (Mus musculus), cluster 3.4 [TaxId:10090] [88530] (4 PDB entries)
    14. 2741296Species 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. 2741585Species Norway rat (Rattus norvegicus) [TaxId:10116] [88532] (14 PDB entries)
    16. 2741608Species Synthetic construct [TaxId:32630] [158859] (2 PDB entries)
  16. 2741614Immunoglobulin 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. 2741615Species Chinese hamster (Cricetulus griseus) [TaxId:10029] [88542] (1 PDB entry)
    2. 2741618Species 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. 2741627Species Human (Homo sapiens), cluster 2 [TaxId:9606] [88536] (10 PDB entries)
    4. 2741642Species Human (Homo sapiens), cluster 3.1 [TaxId:9606] [88537] (1 PDB entry)
    5. 2741644Species Human (Homo sapiens), cluster 3.2 [TaxId:9606] [88538] (1 PDB entry)
    6. 2741646Species Human (Homo sapiens), cluster 4 [TaxId:9606] [88539] (23 PDB entries)
    7. 2741692Species 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. 2741706Species Mouse (Mus musculus) [TaxId:10090] [88541] (36 PDB entries)
    9. 2741756Species Norway rat (Rattus norvegicus) [TaxId:10116] [101504] (7 PDB entries)
  17. 2741777Immunoreceptor CTLA-4 (CD152), N-terminal fragment [48939] (2 species)
    1. 2741778Species Human (Homo sapiens) [TaxId:9606] [48940] (9 PDB entries)
    2. 2741790Species Mouse (Mus musculus) [TaxId:10090] [48941] (3 PDB entries)
  18. 2741800Junction adhesion molecule, JAM, N-terminal domain [48747] (2 species)
    1. 2741801Species Human (Homo sapiens) [TaxId:9606] [89180] (1 PDB entry)
    2. 2741804Species Mouse (Mus musculus) [TaxId:10090] [48748] (1 PDB entry)
  19. 2741806Kin of IRRE-like protein 3, KIRREL3 [158867] (1 species)
  20. 2741809Myelin membrane adhesion molecule P0 [48728] (1 species)
  21. 2741812Myelin oligodendrocyte glycoprotein (MOG) [89174] (1 species)
  22. 2741819N-terminal domain of sialic acid binding Ig-like lectin 7 (SIGLEC-7, p75/AIRM1) [89176] (1 species)
  23. 2741827N-terminal domain of sialoadhesin [48732] (1 species)
  24. 2741837NK cell activating receptor NKP44 [89178] (1 species)
    a triggering partner in natural cytotoxicity
  25. 2741840Novel antigen receptor (against lysozyme) [110042] (1 species)
  26. 2741846Novel antigen receptor 12Y-1 [110044] (1 species)
  27. 2741849Novel antigen receptor 12Y-2 [110046] (1 species)
  28. 2741853Polymeric-immunoglobulin receptor, PIGR [117038] (1 species)
  29. 2741861Programmed cell death protein 1, PD1, extracellular domain [101510] (2 species)
    1. 2741862Species Human (Homo sapiens) [TaxId:9606] [256383] (17 PDB entries)
    2. 2741888Species Mouse (Mus musculus) [TaxId:10090] [101511] (5 PDB entries)
  30. 2741896T-cell antigen receptor [48933] (6 species)
    sequences may differ within each classified species
    1. 2741897Species Human (Homo sapiens), alpha-chain [TaxId:9606] [48935] (21 PDB entries)
    2. 2741924Species Human (Homo sapiens), beta-chain [TaxId:9606] [48937] (30 PDB entries)
    3. 2741978Species Human (Homo sapiens), delta-chain [TaxId:9606] [48938] (3 PDB entries)
    4. 2741987Species Human (Homo sapiens), gamma-chain [TaxId:9606] [63651] (3 PDB entries)
    5. 2742002Species Mouse (Mus musculus), alpha-chain [TaxId:10090] [48934] (22 PDB entries)
    6. 2742041Species Mouse (Mus musculus), beta-chain [TaxId:10090] [48936] (28 PDB entries)
  31. 2742085TREM-1 (triggering receptor expressed on myeloid cells 1) [101506] (2 species)
    1. 2742086Species Human (Homo sapiens) [TaxId:9606] [101507] (2 PDB entries)
      Uniprot Q9NP99 21-133
    2. 2742093Species Mouse (Mus musculus) [TaxId:10090] [117037] (1 PDB entry)
      Uniprot Q9JKE2 25-134
  32. 2742096Tyrosine-protein kinase receptor tyro3, N-terminal domain [101508] (1 species)
  33. 2742100automated matches [190119] (24 species)
    not a true protein
    1. 2742101Species Camel (Camelus dromedarius) [TaxId:9838] [187219] (42 PDB entries)
    2. 2742186Species Camelus bactrianus [TaxId:9837] [371849] (6 PDB entries)
    3. 2742196Species Cow (Bos taurus) [TaxId:9913] [197337] (3 PDB entries)
    4. 2742202Species Cricetulus migratorius [TaxId:10032] [419867] (1 PDB entry)
    5. 2742207Species Dogfish (Squalus acanthias) [TaxId:7797] [226656] (2 PDB entries)
    6. 2742211Species Escherichia coli [TaxId:83333] [354477] (1 PDB entry)
    7. 2742214Species Human (Homo sapiens) [TaxId:9606] [188740] (705 PDB entries)
    8. 2743664Species Human herpesvirus 1 [TaxId:10299] [256116] (1 PDB entry)
    9. 2743666Species Human herpesvirus 2 [TaxId:10313] [259821] (1 PDB entry)
    10. 2743669Species Human herpesvirus 2 [TaxId:10315] [256151] (1 PDB entry)
    11. 2743671Species Llama (Lama glama) [TaxId:9844] [187485] (245 PDB entries)
    12. 2744165Species Llama glama [TaxId:9844] [236993] (3 PDB entries)
    13. 2744174Species Macaca mulatta [TaxId:9541] [188468] (1 PDB entry)
    14. 2744177Species Mouse (Mus musculus) [TaxId:10090] [186842] (621 PDB entries)
    15. 2745381Species Norway rat (Rattus norvegicus) [TaxId:10116] [187415] (25 PDB entries)
    16. 2745421Species Nurse shark (Ginglymostoma cirratum) [TaxId:7801] [187220] (4 PDB entries)
    17. 2745429Species Ornithorhynchus anatinus [TaxId:9258] [228732] (1 PDB entry)
    18. 2745431Species Pig (Sus scrofa) [TaxId:9823] [322548] (1 PDB entry)
    19. 2745434Species Rabbit (Oryctolagus cuniculus) [TaxId:9986] [331472] (6 PDB entries)
    20. 2745446Species Rat (Rattus rattus) [TaxId:10117] [225551] (1 PDB entry)
    21. 2745451Species Rhesus monkey (Macaca mulatta) [TaxId:9544] [377132] (6 PDB entries)
    22. 2745461Species Spotted wobbegong (Orectolobus maculatus) [TaxId:168098] [187564] (9 PDB entries)
    23. 2745477Species Vicugna pacos [TaxId:30538] [189756] (82 PDB entries)
    24. 3085086Species Lamium maculatum [TaxId:53163] [421403] (2 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):