PDB entry 3rug

View 3rug on RCSB PDB site
Description: Crystal structure of Valpha10-Vbeta8.1 NKT TCR in complex with CD1d-alphaglucosylceramide (C20:2)
Class: immune system
Keywords: mouse CD1d, mouse NKT, IMMUNE SYSTEM
Deposited on 2011-05-05, released 2011-08-03
The last revision prior to the SCOPe 2.06 freeze date was dated 2011-08-03, with a file datestamp of 2011-07-29.
Experiment type: XRAY
Resolution: 2.2 Å
R-factor: 0.212
AEROSPACI score: 0.37 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Antigen-presenting glycoprotein CD1d1
    Species: Mus musculus [TaxId:10090]
    Gene: Cd1d1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P11609 (Start-278)
      • expression tag (279-295)
    Domains in SCOPe 2.06: d3ruga1, d3ruga2, d3ruga3
  • Chain 'B':
    Compound: beta-2 microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3rugb_
  • Chain 'C':
    Compound: Antigen-presenting glycoprotein CD1d1
    Species: Mus musculus [TaxId:10090]
    Gene: Cd1d1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P11609 (Start-278)
      • expression tag (279-294)
    Domains in SCOPe 2.06: d3rugc1, d3rugc2, d3rugc3
  • Chain 'D':
    Compound: beta-2 microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3rugd_
  • Chain 'E':
    Compound: Valpha10(mouse variable domain, human constant domain)
    Species: Mus musculus, Homo sapiens [TaxId:10090, 9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3RUG
    Domains in SCOPe 2.06: d3ruge1, d3ruge2
  • Chain 'F':
    Compound: Vbeta8.1(mouse variable domain, human constant domain)
    Species: Mus musculus, Homo sapiens [TaxId:10090, 9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3RUG
    Domains in SCOPe 2.06: d3rugf1, d3rugf2
  • Chain 'G':
    Compound: Valpha10(mouse variable domain, human constant domain)
    Species: Mus musculus, Homo sapiens [TaxId:10090, 9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3RUG
    Domains in SCOPe 2.06: d3rugg1, d3rugg2
  • Chain 'H':
    Compound: Vbeta8.1(mouse variable domain, human constant domain)
    Species: Mus musculus, Homo sapiens [TaxId:10090, 9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3RUG
    Domains in SCOPe 2.06: d3rugh1, d3rugh2
  • Heterogens: DB6, NAG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3rugA (A:)
    seaqqknytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsn
    qqweklqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvaf
    qgkyvvrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagk
    sdlekqekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpn
    adetwylqatldveageeaglacrvkhsslggqdiilywgslhhildaqkmvwnhrhhhh
    hh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3rugA (A:)
    ytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqweklq
    hmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyvvr
    fwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlekqe
    kpvawlssvpsghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetwylqat
    ldveageeaglacrvkhsslggqdiilywgslhhildaqkmvwnhr
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3rugB (B:)
    iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
    sfyilahteftptetdtyacrvkhasmaepktvywdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >3rugB (B:)
    qktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdws
    fyilahteftptetdtyacrvkhasmaepktvywdrdm
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3rugC (C:)
    seaqqknytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsn
    qqweklqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvaf
    qgkyvvrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagk
    sdlekqekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpn
    adetwylqatldveageeaglacrvkhsslggqdiilywgslhhildaqkmvwnhrhhhh
    hh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3rugC (C:)
    ytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqweklq
    hmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyvvr
    fwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlekqe
    kpvawlssvpsghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetwylqat
    ldveageeaglacrvkhsslggqdiilywgslhhildaqkmvwnh
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3rugD (D:)
    iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
    sfyilahteftptetdtyacrvkhasmaepktvywdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >3rugD (D:)
    qktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdws
    fyilahteftptetdtyacrvkhasmaepktvywdrdm
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3rugE (E:)
    gqqveqspaslvlqegenaelqctysttlnsmqwfyqrpggrlvsllyspswaeqrggrl
    tssaasnesrsslhisssqitdsgtylcaiasssfsklvfgqgtslsvvpniqnpdpavy
    qlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsnksd
    facanafnnsiipedtffpspess
    

    Sequence, based on observed residues (ATOM records): (download)
    >3rugE (E:)
    qveqspaslvlqegenaelqctysttlnsmqwfyqrpggrlvsllyspswaeqrggrlts
    saasnesrsslhisssqitdsgtylcaiasssfsklvfgqgtslsvvpniqnpdpavyql
    rdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsnksdfa
    canafnnsiipedtffps
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >3rugF (F:)
    eaavtqsprskvavtggkvtlschqtnnhdymywyrqdtghglrlihysyvadstekgdi
    pdgykasrpsqenfslilelaslsqtavyfcasrlggyeqyfgpgtrltvledlknvfpp
    evavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpal
    ndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgra
    d
    

    Sequence, based on observed residues (ATOM records): (download)
    >3rugF (F:)
    avtqsprskvavtggkvtlschqtnnhdymywyrqdtghglrlihysyvadstekgdipd
    gykasrpsqenfslilelaslsqtavyfcasrlggyeqyfgpgtrltvledlknvfppev
    avfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpalsr
    yalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgra
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >3rugG (G:)
    gqqveqspaslvlqegenaelqctysttlnsmqwfyqrpggrlvsllyspswaeqrggrl
    tssaasnesrsslhisssqitdsgtylcaiasssfsklvfgqgtslsvvpniqnpdpavy
    qlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsnksd
    facanafnnsiipedtffpspess
    

    Sequence, based on observed residues (ATOM records): (download)
    >3rugG (G:)
    qveqspaslvlqegenaelqctysttlnsmqwfyqrpggrlvsllyspswaeqrggrlts
    saasnesrsslhisssqitdsgtylcaiasssfsklvfgqgtslsvvpniqnpdpavyql
    rdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsnksdfa
    canafnnsiipedtffps
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >3rugH (H:)
    eaavtqsprskvavtggkvtlschqtnnhdymywyrqdtghglrlihysyvadstekgdi
    pdgykasrpsqenfslilelaslsqtavyfcasrlggyeqyfgpgtrltvledlknvfpp
    evavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpal
    ndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgra
    d
    

    Sequence, based on observed residues (ATOM records): (download)
    >3rugH (H:)
    avtqsprskvavtggkvtlschqtnnhdymywyrqdtghglrlihysyvadstekgdipd
    gykasrpsqenfslilelaslsqtavyfcasrlggyeqyfgpgtrltvledlknvfppev
    avfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpalsr
    yalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgra