PDB entry 3o8x

View 3o8x on RCSB PDB site
Description: Recognition of Glycolipid Antigen by iNKT Cell TCR
Class: immune system
Keywords: antigen presentation, glycolipid, NKT cells, IMMUNE SYSTEM
Deposited on 2010-08-03, released 2010-09-29
The last revision prior to the SCOPe 2.03 freeze date was dated 2010-10-13, with a file datestamp of 2010-10-08.
Experiment type: XRAY
Resolution: 2.74 Å
R-factor: 0.198
AEROSPACI score: 0.29 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Antigen-presenting glycoprotein CD1d1
    Species: Mus musculus [TaxId:10090]
    Gene: Cd1.1, CD1d, Cd1d1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d3o8xa1, d3o8xa2
  • Chain 'B':
    Compound: beta-2 microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2m, beta-2-microglobulin, mCG_11606, RP23-34E24.5-001
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d3o8xb_
  • Chain 'C':
    Compound: Valpha14 chimera (Mouse variable domain, Human T-cell receptor alpha chain C region constant domain)
    Species: Mus musculus, Homo sapiens [TaxId:10090,9606]
    Gene: TRAC, TCRA
    Database cross-references and differences (RAF-indexed):
    • PDB 3O8X (Start-120)
    • Uniprot P01848 (121-End)
      • engineered mutation (162)
    Domains in SCOPe 2.03: d3o8xc1, d3o8xc2
  • Chain 'D':
    Compound: Vbeta8.2 chimera (Mouse variable domain, Human T-cell receptor beta-2 chain C region constant domain)
    Species: Mus musculus, Homo sapiens [TaxId:10090,9606]
    Gene: TRBC2, TCRBC2
    Database cross-references and differences (RAF-indexed):
    • PDB 3O8X (Start-129)
    • Uniprot A0A5B9 (130-240)
      • engineered mutation (168)
      • engineered mutation (186)
    Domains in SCOPe 2.03: d3o8xd1, d3o8xd2
  • Heterogens: GSL, NAG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3o8xA (A:)
    seaqqknytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsn
    qqweklqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvaf
    qgkyvvrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagk
    sdlekqekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpn
    adetwylqatldveageeaglacrvkhsslggqdiilywhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3o8xA (A:)
    nytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwekl
    qhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyvv
    rfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlekq
    ekpvawlssvpsrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetwylqatl
    dveageeaglacrvkhsslggqdiilyw
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3o8xB (B:)
    iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
    sfyilahteftptetdtyacrvkhasmaepktvywdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >3o8xB (B:)
    qktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdws
    fyilahteftptetdtyacrvkhasmaepktvywdr
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3o8xC (C:)
    mktqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsn
    grysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnp
    dpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaw
    snksdfacanafnnsiipedtffpspess
    

    Sequence, based on observed residues (ATOM records): (download)
    >3o8xC (C:)
    tqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsngr
    ysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnpdp
    avyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsn
    ksdfacanafnnsiipedtffps
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3o8xD (D:)
    meaavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgd
    ipdgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtp
    pkvslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpa
    lndsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgr
    a
    

    Sequence, based on observed residues (ATOM records): (download)
    >3o8xD (D:)
    aavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgdip
    dgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtppk
    vslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpaln
    dsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgra