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: 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 ...

    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: 

    Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK. jamie.rossjohn@monash.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinE [auth A], A [auth H]107Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
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Find proteins for P61769 (Homo sapiens)
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PHAROS:  P61769
GTEx:  ENSG00000166710
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell receptor alpha variable 4,TCR alpha chainF [auth B], B [auth C]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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Entity ID: 3
MoleculeChainsSequence 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 
Go to UniProtKB:  A0A0B4J1U6
PHAROS:  A0A0B4J1U6
GTEx:  ENSG00000211716
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, B-7 alpha chainH [auth F], D [auth G]362Homo sapiensMutation(s): 0 
Gene Names: HLA-B, HLAB
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Find proteins for P01889 (Homo sapiens)
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PHAROS:  P01889
GTEx:  ENSG00000234745
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
ALA-PRO-ARG-GLY-PRO-HIS-GLY-GLY-ALA-ALA-SER-GLY-LEUJ [auth P], I [auth Q]13Homo sapiensMutation(s): 0 
Gene Names: CTAG1A, CTAG, CTAG1, ESO1, LAGE2, LAGE2A, CTAG1B, LAGE2B
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Find proteins for P78358 (Homo sapiens)
Explore P78358 
Go to UniProtKB:  P78358
PHAROS:  P78358
GTEx:  ENSG00000184033ENSG00000268651
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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