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:  
    6AT6, 6AT5, 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 imm ...

    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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinAH107Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell receptor alpha variable 4,TCR alpha chainBC202Homo sapiensMutation(s): 0 
Gene Names: TRAV4
Find proteins for A0A0B4J268 (Homo sapiens)
Explore A0A0B4J268 
Go to UniProtKB:  A0A0B4J268
NIH Common Fund Data Resources
PHAROS  A0A0B4J268
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell receptor beta variable 9,TCR beta chainDE245Homo sapiensMutation(s): 0 
Gene Names: TRBV9
Find proteins for A0A0B4J1U6 (Homo sapiens)
Explore A0A0B4J1U6 
Go to UniProtKB:  A0A0B4J1U6
NIH Common Fund Data Resources
PHAROS  A0A0B4J1U6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, B-7 alpha chainFG362Homo sapiensMutation(s): 0 
Gene Names: HLA-BHLAB
Find proteins for P01889 (Homo sapiens)
Explore P01889 
Go to UniProtKB:  P01889
NIH Common Fund Data Resources
PHAROS  P01889
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
ALA-PRO-ARG-GLY-PRO-HIS-GLY-GLY-ALA-ALA-SER-GLY-LEUPQ13Homo sapiensMutation(s): 0 
Gene Names: CTAG1ACTAGCTAG1ESO1LAGE2LAGE2ACTAG1BLAGE2B
Find proteins for P78358 (Homo sapiens)
Explore P78358 
Go to UniProtKB:  P78358
NIH Common Fund Data Resources
PHAROS  P78358
Protein Feature View
Expand
  • Reference Sequence
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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