PDB entry 4y4h

View 4y4h on RCSB PDB site
Description: Crystal structure of the mCD1d/GCK152/iNKTCR ternary complex
Class: immune system
Keywords: MHC-fold, Ig-fold, glycolipid antigen presentation, T cell receptor, IMMUNE SYSTEM
Deposited on 2015-02-10, released 2015-05-27
The last revision prior to the SCOPe 2.05 freeze date was dated 2015-05-27, with a file datestamp of 2015-05-22.
Experiment type: XRAY
Resolution: 3.1 Å
R-factor: N/A
AEROSPACI score: 0.12 (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): Domains in SCOPe 2.05: d4y4ha1, d4y4ha2
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d4y4hb_
  • Chain 'C':
    Compound: Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain/ human constant domain)
    Species: Mus musculus, Homo sapiens [TaxId:10090, 9606]
    Gene: Trav11, Trav11d, HDCMA22P
    Database cross-references and differences (RAF-indexed):
    • PDB 4Y4H
    Domains in SCOPe 2.05: d4y4hc1, d4y4hc2
  • Chain 'D':
    Compound: Chimeric TCR Vbeta8.2 chain (mouse variable domain/ human constant domain)
    Species: Mus musculus, Homo sapiens [TaxId:10090,9606]
    Gene: TRBC2, TCRBC2
    Database cross-references and differences (RAF-indexed):
    • PDB 4Y4H (Start-240)
    Domains in SCOPe 2.05: d4y4hd1, d4y4hd2
  • Chain 'E':
    Compound: Antigen-presenting glycoprotein CD1d1
    Species: Mus musculus [TaxId:10090]
    Gene: Cd1d1, Cd1.1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d4y4he1, d4y4he2
  • Chain 'F':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d4y4hf_
  • Chain 'G':
    Compound: Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain/ human constant domain)
    Species: Mus musculus, Homo sapiens [TaxId:10090, 9606]
    Gene: Trav11, Trav11d, HDCMA22P
    Database cross-references and differences (RAF-indexed):
    • PDB 4Y4H
    Domains in SCOPe 2.05: d4y4hg1, d4y4hg2
  • Chain 'H':
    Compound: Chimeric TCR Vbeta8.2 chain (mouse variable domain/ human constant domain)
    Species: Mus musculus, Homo sapiens [TaxId:10090,9606]
    Gene: TRBC2, TCRBC2
    Database cross-references and differences (RAF-indexed):
    • PDB 4Y4H (Start-240)
    Domains in SCOPe 2.05: d4y4hh1, d4y4hh2
  • Heterogens: NAG, 49X

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >4y4hA (A:)
seaqqknytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsn
qqweklqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvaf
qgkyvvrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagk
sdlekqekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpn
adetwylqatldveageeaglacrvkhsslggqdiilywhhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >4y4hA (A:)
nytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwekl
qhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyvv
rfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlekq
ekpvawlssvprqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetwylqatld
veageeaglacrvkhsslggqdiilyw

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >4y4hB (B:)
iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
sfyilahteftptetdtyacrvkhasmaepktvywdrdm

    Sequence, based on observed residues (ATOM records): (download) 
    >4y4hB (B:)
qktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdws
fyilahteftptetdtyacrvkhasmaepktvywdr

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >4y4hC (C:)
mktqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsn
grysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnp
dpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaw
snksdfacanafnnsiipedtffpspess

    Sequence, based on observed residues (ATOM records): (download) 
    >4y4hC (C:)
tqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsngr
ysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnpdp
avyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsn
kdfacanafnnsiipedtffps

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >4y4hD (D:)
meaavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgd
ipdgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtp
pkvslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpa
lndsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgr
a

    Sequence, based on observed residues (ATOM records): (download) 
    >4y4hD (D:)
aavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgdip
dgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtppk
vslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpaln
dsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgra

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >4y4hE (E:)
seaqqknytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsn
qqweklqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvaf
qgkyvvrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagk
sdlekqekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpn
adetwylqatldveageeaglacrvkhsslggqdiilywhhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >4y4hE (E:)
nytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwekl
qhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyvv
rfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlekq
ekpvawlssvprqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetwylqatld
veageeaglacrvkhsslggqdiilyw

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >4y4hF (F:)
iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
sfyilahteftptetdtyacrvkhasmaepktvywdrdm

    Sequence, based on observed residues (ATOM records): (download) 
    >4y4hF (F:)
qktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdws
fyilahteftptetdtyacrvkhasmaepktvywdr

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >4y4hG (G:)
mktqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsn
grysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnp
dpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaw
snksdfacanafnnsiipedtffpspess

    Sequence, based on observed residues (ATOM records): (download) 
    >4y4hG (G:)
tqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsngr
ysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnpdp
avyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsn
kdfacanafnnsiipedtffps

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >4y4hH (H:)
meaavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgd
ipdgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtp
pkvslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpa
lndsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgr
a

    Sequence, based on observed residues (ATOM records): (download) 
    >4y4hH (H:)
aavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgdip
dgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtppk
vslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpaln
dsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgra