PDB entry 3huj

View 3huj on RCSB PDB site
Description: Crystal structure of human CD1d-alpha-Galactosylceramide in complex with semi-invariant NKT cell receptor
Class: immune system
Keywords: CD1d, NKT T cell receptor, alpha-galactosylceramide, protein receptor complex, Cell membrane, Disulfide bond, Endosome, Glycoprotein, Host-virus interaction, Immune response, Immunoglobulin domain, Innate immunity, Lysosome, Membrane, Transmembrane, Disease mutation, Glycation, MHC I, Pyrrolidone carboxylic acid, Secreted, IMMUNE SYSTEM
Deposited on 2009-06-14, released 2009-07-28
The last revision prior to the SCOPe 2.03 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-25.
Experiment type: XRAY
Resolution: 2.5 Å
R-factor: 0.219
AEROSPACI score: 0.3 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: T-cell surface glycoprotein CD1d
    Species: Homo sapiens [TaxId:9606]
    Gene: CD1D
    Database cross-references and differences (RAF-indexed):
    • Uniprot P15813 (Start-277)
      • expression tag (278-280)
    Domains in SCOPe 2.03: d3huja1, d3huja2
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d3hujb_
  • Chain 'C':
    Compound: T-cell surface glycoprotein CD1d
    Species: Homo sapiens [TaxId:9606]
    Gene: CD1D
    Database cross-references and differences (RAF-indexed):
    • Uniprot P15813 (Start-277)
      • expression tag (278)
    Domains in SCOPe 2.03: d3hujc1, d3hujc2
  • Chain 'D':
    Compound: Beta-2-microglobulin
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d3hujd_
  • Chain 'E':
    Compound: NKT15 T cell receptor alpha-chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3HUJ
    Domains in SCOPe 2.03: d3huje1, d3huje2
  • Chain 'F':
    Compound: NKT15 T cell receptor beta-chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3HUJ (Start-245)
    Domains in SCOPe 2.03: d3hujf1, d3hujf2
  • Chain 'G':
    Compound: NKT15 T cell receptor alpha-chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3HUJ
    Domains in SCOPe 2.03: d3hujg1, d3hujg2
  • Chain 'H':
    Compound: NKT15 T cell receptor beta-chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3HUJ (Start-245)
    Domains in SCOPe 2.03: d3hujh1, d3hujh2
  • Heterogens: NAG, AGH, NDG, MG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3hujA (A:)
    spgvpqrlfplrclqissfansswtrtdglawlgelqthswsndsdtvrslkpwsqgtfs
    dqqwetlqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgnasnnffhvafq
    gkdilsfqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllngtcpqfvsgllesgks
    elkkqvkpkawlsrgpspgpgrlllvchvsgfypkpvwvkwmrgeqeqqgtqpgdilpna
    detwylratldvvageaaglscrvkhsslegqdivlywhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3hujA (A:)
    rlfplrclqissfansswtrtdglawlgelqthswsndsdtvrslkpwsqgtfsdqqwet
    lqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgnasnnffhvafqgkdils
    fqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllngtcpqfvsgllesgkselkkqv
    kpkawlsrgpspgpgrlllvchvsgfypkpvwvkwmrgeqeqqgtqpgdilpnadetwyl
    ratldvvageaaglscrvkhsslegqdivlywhhh
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3hujB (B:)
    iqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskdw
    sfyllyyteftptekdeyacrvnhvtlsqpkivkwdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >3hujB (B:)
    iqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskdw
    sfyllyyteftptekdeyacrvnhvtlsqpkivkwdr
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3hujC (C:)
    spgvpqrlfplrclqissfansswtrtdglawlgelqthswsndsdtvrslkpwsqgtfs
    dqqwetlqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgnasnnffhvafq
    gkdilsfqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllngtcpqfvsgllesgks
    elkkqvkpkawlsrgpspgpgrlllvchvsgfypkpvwvkwmrgeqeqqgtqpgdilpna
    detwylratldvvageaaglscrvkhsslegqdivlywhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3hujC (C:)
    qrlfplrclqissfansswtrtdglawlgelqthswsndsdtvrslkpwsqgtfsdqqwe
    tlqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgnasnnffhvafqgkdil
    sfqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllngtcpqfvsgllesgkselkkq
    vkpkawlsrgpspgpgrlllvchvsgfypkpvwvkwmrgeqeqqgtqpgdilpnadetwy
    lratldvvageaaglscrvkhsslegqdivlywh
    

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3hujD (D:)
    iqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskdw
    sfyllyyteftptekdeyacrvnhvtlsqpkivkwdrdm
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3hujE (E:)
    mknqveqspqsliilegknctlqcnytvspfsnlrwykqdtgrgpvsltimtfsentksn
    grytatldadtkqsslhitasqlsdsasyicvvsdrgstlgrlyfgrgtqltvwpdiqnp
    dpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaw
    snksdfacanafnnsiipedtffpspess
    

    Sequence, based on observed residues (ATOM records): (download)
    >3hujE (E:)
    nqveqspqsliilegknctlqcnytvspfsnlrwykqdtgrgpvsltimtfsentksngr
    ytatldadtkqsslhitasqlsdsasyicvvsdrgstlgrlyfgrgtqltvwpdiqnpdp
    avyqlrdssdkvclftdfdsqtnvsqsdsdvyitdkcvldmrsmdfksnsavawsnksdf
    acanafnnsiipedtffps
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >3hujF (F:)
    meadiyqtprylvigtgkkitlecsqtmghdkmywyqqdpgmelhlihysygvnstekgd
    lssestvsrirtehfpltlesarpshtsqylcassglrdrglyeqyfgpgtrltvtedlk
    nvfppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplk
    eqpalndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsae
    awgrad
    

    Sequence, based on observed residues (ATOM records): (download)
    >3hujF (F:)
    adiyqtprylvigtgkkitlecsqtmghdkmywyqqdpgmelhlihysygvnstekgdls
    sestvsrirtehfpltlesarpshtsqylcassglrdlyeqyfgpgtrltvtedlknvfp
    pevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpa
    lndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgr
    ad
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >3hujG (G:)
    mknqveqspqsliilegknctlqcnytvspfsnlrwykqdtgrgpvsltimtfsentksn
    grytatldadtkqsslhitasqlsdsasyicvvsdrgstlgrlyfgrgtqltvwpdiqnp
    dpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaw
    snksdfacanafnnsiipedtffpspess
    

    Sequence, based on observed residues (ATOM records): (download)
    >3hujG (G:)
    nqveqspqsliilegknctlqcnytvspfsnlrwykqdtgrgpvsltimtfsentksngr
    ytatldadtkqsslhitasqlsdsasyicvvsdrgstlgrlyfgrgtqltvwpdiqnpdp
    avyqlrdskssdsvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsnk
    sdfacanafnnsiipedtffps
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >3hujH (H:)
    meadiyqtprylvigtgkkitlecsqtmghdkmywyqqdpgmelhlihysygvnstekgd
    lssestvsrirtehfpltlesarpshtsqylcassglrdrglyeqyfgpgtrltvtedlk
    nvfppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplk
    eqpalndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsae
    awgrad
    

    Sequence, based on observed residues (ATOM records): (download)
    >3hujH (H:)
    eadiyqtprylvigtgkkitlecsqtmghdkmywyqqdpgmelhlihysygvnstekgdl
    ssestvsrirtehfpltlesarpshtsqylcassglrdrglyeqyfgpgtrltvtedlkn
    vfppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplke
    qpalndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaea
    wgrad