PDB entry 3o9w

View 3o9w on RCSB PDB site
Description: Recognition of a Glycolipid Antigen by the iNKT Cell TCR
Class: immune system
Keywords: antigen presentation, glycolipid, NKT cells, IMMUNE SYSTEM
Deposited on 2010-08-04, released 2010-09-29
The last revision prior to the SCOPe 2.07 freeze date was dated 2017-06-28, with a file datestamp of 2017-06-23.
Experiment type: XRAY
Resolution: 2.8 Å
R-factor: N/A
AEROSPACI score: 0.16 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Antigen-presenting glycoprotein CD1d1
    Species: Mus musculus [TaxId:10090]
    Gene: Cd1d1, Cd1.1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P11609 (Start-278)
      • variant (200)
    Domains in SCOPe 2.07: d3o9wa1, d3o9wa2
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3o9wb_
  • Chain 'C':
    Compound: Valpha14 chimera (Mouse variable domain, Human T-cell receptor alpha chain C region constant domain)
    Species: Homo sapiens [TaxId:9606]
    Gene: TRAC, TCRA
    Database cross-references and differences (RAF-indexed):
    • PDB 3O9W (Start-120)
    • Uniprot P01848 (121-End)
      • engineered mutation (162)
    Domains in SCOPe 2.07: d3o9wc1, d3o9wc2
  • Chain 'D':
    Compound: Vbeta8.2 chimera (Mouse variable domain, Human T-cell receptor beta-2 chain C region constant domain)
    Species: Homo sapiens [TaxId:9606]
    Gene: TRBC2, TCRBC2
    Database cross-references and differences (RAF-indexed):
    • PDB 3O9W (Start-129)
    • Uniprot A0A5B9 (130-240)
      • engineered mutation (168)
      • engineered mutation (186)
    Domains in SCOPe 2.07: d3o9wd1, d3o9wd2
  • Heterogens: NAG, FUC, 1O2, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3o9wA (A:)
    seaqqknytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsn
    qqweklqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvaf
    qgkyvvrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagk
    sdlekqekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpn
    adetwylqatldveageeaglacrvkhsslggqdiilywhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3o9wA (A:)
    knytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwek
    lqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyv
    vrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlek
    qekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetw
    ylqatldveageeaglacrvkhsslggqdiilyw
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3o9wB (B:)
    iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
    sfyilahteftptetdtyacrvkhasmaepktvywdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >3o9wB (B:)
    qktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdws
    fyilahteftptetdtyacrvkhasmaepktvywdrd
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3o9wC (C:)
    mktqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsn
    grysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnp
    dpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaw
    snksdfacanafnnsiipedtffpspess
    

    Sequence, based on observed residues (ATOM records): (download)
    >3o9wC (C:)
    tqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsngr
    ysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnpdp
    avyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsn
    ksdfacanafnnsiipedtffps
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3o9wD (D:)
    meaavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgd
    ipdgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtp
    pkvslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpa
    lndsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgr
    a
    

    Sequence, based on observed residues (ATOM records): (download)
    >3o9wD (D:)
    aavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgdip
    dgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtppk
    vslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpaln
    dsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgra