6AVG

Crystal structure of the KFJ37 TCR-NY-ESO-1-HLA-B*07:02 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Divergent T-cell receptor recognition modes of a HLA-I restricted extended tumour-associated peptide.

Chan, K.F.Gully, B.S.Gras, S.Beringer, D.X.Kjer-Nielsen, L.Cebon, J.McCluskey, J.Chen, W.Rossjohn, J.

(2018) Nat Commun 9: 1026-1026

  • DOI: https://doi.org/10.1038/s41467-018-03321-w
  • Primary Citation of Related Structures:  
    6AT5, 6AT6, 6AVF, 6AVG

  • PubMed Abstract: 

    Human leukocyte antigen (HLA)-I molecules generally bind short peptides (8-10 amino acids), although extended HLA-I restricted peptides (>10 amino acids) can be presented to T cells. However, the function of such extended HLA-I epitopes in tumour immunity, and how they would be recognised by T-cell receptors (TCR) remains unclear. Here we show that the structures of two distinct TCRs (TRAV4 + TRAJ21 + -TRBV28 + TRBJ2-3 + and TRAV4 + TRAJ8 + -TRBV9 + TRBJ2-1 + ), originating from a polyclonal T-cell repertoire, bind to HLA-B*07:02, presenting a 13-amino-acid-long tumour-associated peptide, NY-ESO-1 60-72 . Comparison of the structures reveals that the two TCRs differentially binds NY-ESO-1 60-72 -HLA-B*07:02 complex, and induces differing extent of conformational change of the NY-ESO-1 60-72 epitope. Accordingly, polyclonal TCR usage towards an extended HLA-I restricted tumour epitope translates to differing TCR recognition modes, whereby extensive flexibility at the TCR-pHLA-I interface engenders recognition.


  • Organizational Affiliation

    Olivia Newton-John Cancer Research Institute, and School of Cancer Medicine, La Trobe University, Heidelberg, VIC, 3084, Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulinA [auth H],
E [auth A]
107Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
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Find proteins for P61769 (Homo sapiens)
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PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell receptor alpha variable 4,TCR alpha chainB [auth C],
F [auth B]
202Homo sapiensMutation(s): 0 
Gene Names: TRAV4
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Find proteins for A0A0B4J268 (Homo sapiens)
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PHAROS:  A0A0B4J268
GTEx:  ENSG00000211778 
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UniProt GroupA0A0B4J268
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell receptor beta variable 9,TCR beta chainC [auth D],
G [auth E]
245Homo sapiensMutation(s): 0 
Gene Names: TRBV9
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Find proteins for A0A0B4J1U6 (Homo sapiens)
Explore A0A0B4J1U6 
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PHAROS:  A0A0B4J1U6
GTEx:  ENSG00000211716 
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UniProt GroupA0A0B4J1U6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, B-7 alpha chainD [auth G],
H [auth F]
362Homo sapiensMutation(s): 0 
Gene Names: HLA-BHLAB
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Find proteins for P01889 (Homo sapiens)
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PHAROS:  P01889
GTEx:  ENSG00000234745 
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UniProt GroupP01889
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-PRO-ARG-GLY-PRO-HIS-GLY-GLY-ALA-ALA-SER-GLY-LEUI [auth Q],
J [auth P]
13Homo sapiensMutation(s): 0 
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Find proteins for P78358 (Homo sapiens)
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.805α = 94.22
b = 74.863β = 97.88
c = 96.276γ = 90.16
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-03-28
    Changes: Data collection, Database references