6TRO

Crystal structure of the T-cell receptor GVY01 bound to HLA A2*01-GVYDGREHTV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

T cell receptor interactions with human leukocyte antigen govern indirect peptide selectivity for the cancer testis antigen MAGE-A4.

Coles, C.H.McMurran, C.Lloyd, A.Hock, M.Hibbert, L.Raman, M.C.C.Hayes, C.Lupardus, P.Cole, D.K.Harper, S.

(2020) J Biol Chem 295: 11486-11494

  • DOI: 10.1074/jbc.RA120.014016
  • Primary Citation of Related Structures:  
    6TRN, 6TRO

  • PubMed Abstract: 
  • T cell-mediated immunity is governed primarily by T cell receptor (TCR) recognition of peptide-human leukocyte antigen (pHLA) complexes and is essential for immunosurveillance and disease control. This interaction is generally stabilized by interactions between the HLA surface and TCR germline-encoded complementarity-determining region (CDR) loops 1 and 2, whereas peptide selectivity is guided by direct interactions with the TCR CDR3 loops ...

    T cell-mediated immunity is governed primarily by T cell receptor (TCR) recognition of peptide-human leukocyte antigen (pHLA) complexes and is essential for immunosurveillance and disease control. This interaction is generally stabilized by interactions between the HLA surface and TCR germline-encoded complementarity-determining region (CDR) loops 1 and 2, whereas peptide selectivity is guided by direct interactions with the TCR CDR3 loops. Here, we solved the structure of a newly identified TCR in complex with a clinically relevant peptide derived from the cancer testis antigen melanoma antigen-A4 (MAGE-A4). The TCR bound pHLA in a position shifted toward the peptide's N terminus. This enabled the TCR to achieve peptide selectivity via an indirect mechanism, whereby the TCR sensed the first residue of the peptide through HLA residue Trp-167, which acted as a tunable gateway. Amino acid substitutions at peptide position 1 predicted to alter the HLA Trp-167 side-chain conformation abrogated TCR binding, indicating that this indirect binding mechanism is essential for peptide recognition. These findings extend our understanding of the molecular rules that underpin antigen recognition by TCRs and have important implications for the development of TCR-based therapies.


    Organizational Affiliation

    Immunocore Ltd., Abingdon, United Kingdom stephen.harper@immunocore.com david.cole@immunocore.com.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MHC class I antigenA276Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLA
UniProt
Find proteins for Q53Z42 (Homo sapiens)
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Go to UniProtKB:  Q53Z42
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UniProt GroupQ53Z42
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
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Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MAGE-A4 peptide (amino acids 230-239)C10Homo sapiensMutation(s): 0 
Gene Names: MAGEA4MAGE4
UniProt & NIH Common Fund Data Resources
Find proteins for P43358 (Homo sapiens)
Explore P43358 
Go to UniProtKB:  P43358
PHAROS:  P43358
GTEx:  ENSG00000147381 
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UniProt GroupP43358
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell receptor alpha chainD208Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell receptor beta chainE247Homo sapiensMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 220.04α = 90
b = 220.04β = 90
c = 96.83γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data scaling
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Data collection, Database references, Structure summary