PDB entry 3tvm

View 3tvm on RCSB PDB site
Description: Structure of the mouse CD1d-SMC124-iNKT TCR complex
Class: immune system
Keywords: antigen presentation, glycolipid, NKT cells, IMMUNE SYSTEM
Deposited on 2011-09-20, released 2012-02-01
The last revision prior to the SCOPe 2.07 freeze date was dated 2012-02-01, with a file datestamp of 2012-01-27.
Experiment type: XRAY
Resolution: 2.8 Å
R-factor: 0.226
AEROSPACI score: 0.27 (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 2.07: d3tvma1, d3tvma2
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: BETA-2-MICROGLOBULIN
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01887 (Start-98)
      • variant (84)
    Domains in SCOPe 2.07: d3tvmb_
  • Chain 'C':
    Compound: Valpha14 (mouse variable domain, human constant domain)
    Species: MUS MUSCULUS, HOMO SAPIENS [TaxId:10090, 9606]
    Gene: Valpha14 (mouse variable domain, human constant domain)
    Database cross-references and differences (RAF-indexed):
    • PDB 3TVM
    Domains in SCOPe 2.07: d3tvmc1, d3tvmc2
  • Chain 'D':
    Compound: Vbeta8.2 (mouse variable domain, human constant domain)
    Species: MUS MUSCULUS, HOMO SAPIENS [TaxId:10090, 9606]
    Gene: Vbeta8.2 (mouse variable domain, human constant domain)
    Database cross-references and differences (RAF-indexed):
    • PDB 3TVM (Start-240)
    Domains in SCOPe 2.07: d3tvmd1, d3tvmd2
  • Chain 'E':
    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 2.07: d3tvme1, d3tvme2
  • Chain 'F':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: BETA-2-MICROGLOBULIN
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3tvmf_
  • Chain 'G':
    Compound: Valpha14 (mouse variable domain, human constant domain)
    Species: MUS MUSCULUS, HOMO SAPIENS [TaxId:10090, 9606]
    Gene: Valpha14 (mouse variable domain, human constant domain)
    Database cross-references and differences (RAF-indexed):
    • PDB 3TVM
    Domains in SCOPe 2.07: d3tvmg1, d3tvmg2
  • Chain 'H':
    Compound: Vbeta8.2 (mouse variable domain, human constant domain)
    Species: MUS MUSCULUS, HOMO SAPIENS [TaxId:10090, 9606]
    Gene: Vbeta8.2 (mouse variable domain, human constant domain)
    Database cross-references and differences (RAF-indexed):
    • PDB 3TVM (Start-240)
    Domains in SCOPe 2.07: d3tvmh1, d3tvmh2
  • Heterogens: NAG, 07P, CL, GOL, HOH

PDB Chain Sequences:

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

    Sequence, based on observed residues (ATOM records): (download)
    >3tvmA (A:)
    knytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwek
    lqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyv
    vrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlek
    qekpvawlssvpsshrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetwylq
    atldgeeaglacrvkhsslggqdiilyw
    

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

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

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

    Sequence, based on observed residues (ATOM records): (download)
    >3tvmC (C:)
    tqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsngr
    ysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnpdp
    avyqlrdskssdksvclftdfdsqtnvsdsdvyitdkcvldmrsmdfksnsavawsnksd
    facanafnnsiipedtffps
    

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

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

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

    Sequence, based on observed residues (ATOM records): (download)
    >3tvmE (E:)
    nytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwekl
    qhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemasesflhvafqgkyvvrfwg
    tswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlekqewls
    svplvchvsgfypkpvflpnadetwylqa
    

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

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

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

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

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

    Sequence, based on observed residues (ATOM records): (download)
    >3tvmH (H:)
    eaavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgdi
    pdgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtpp
    kvslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpal
    ndsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgra