6AVG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.193 

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:  

  • 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

    Department of Biochemistry & Genetics, La Trobe Institute of Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia. weisan.chen@latrobe.edu.au.,Department of Biochemistry & Genetics, La Trobe Institute of Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia.,Olivia Newton-John Cancer Research Institute, and School of Cancer Medicine, La Trobe University, Heidelberg, VIC, 3084, Australia. weisan.chen@latrobe.edu.au.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia. jamie.rossjohn@monash.edu.,Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia. jamie.rossjohn@monash.edu.,Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC, 3010, Australia.,Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia.,Olivia Newton-John Cancer Research Institute, and School of Cancer Medicine, La Trobe University, Heidelberg, VIC, 3084, Australia.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.,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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
H, A
107Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
T-cell receptor alpha variable 4,TCR alpha chain
C, B
202N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
T-cell receptor beta variable 9,TCR beta chain
D, E
245N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, B-7 alpha chain
G, F
362Homo sapiensMutation(s): 0 
Gene Names: HLA-B (HLAB)
Find proteins for P01889 (Homo sapiens)
Go to Gene View: HLA-B
Go to UniProtKB:  P01889
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ALA-PRO-ARG-GLY-PRO-HIS-GLY-GLY-ALA-ALA-SER-GLY-LEU
Q, P
13Homo sapiensMutation(s): 0 
Gene Names: CTAG1A, CTAG1B (CTAG, CTAG1, ESO1, LAGE2, LAGE2A, LAGE2B)
Find proteins for P78358 (Homo sapiens)
Go to Gene View: CTAG1A CTAG1B
Go to UniProtKB:  P78358
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.193 
  • 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
XDSdata reduction
PHENIXrefinement
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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