3GSN

Crystal structure of the public RA14 TCR in complex with the HCMV dominant NLV/HLA-A2 epitope


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural bases for the affinity-driven selection of a public TCR against a dominant human cytomegalovirus epitope.

Gras, S.Saulquin, X.Reiser, J.B.Debeaupuis, E.Echasserieau, K.Kissenpfennig, A.Legoux, F.Chouquet, A.Le Gorrec, M.Machillot, P.Neveu, B.Thielens, N.Malissen, B.Bonneville, M.Housset, D.

(2009) J Immunol 183: 430-437

  • DOI: https://doi.org/10.4049/jimmunol.0900556
  • Primary Citation of Related Structures:  
    3GSN, 3GSO, 3GSQ, 3GSR, 3GSU, 3GSV, 3GSW, 3GSX

  • PubMed Abstract: 

    Protective T cell responses elicited along chronic human CMV (HCMV) infections are sometimes dominated by CD8 T cell clones bearing highly related or identical public TCR in unrelated individuals. To understand the principles that guide emergence of these public T cell responses, we have performed structural, biophysical, and functional analyses of an immunodominant public TCR (RA14) directed against a major HLA-A*0201-restricted HCMV Ag (pp65(495-503)) and selected in vivo from a diverse repertoire after chronic stimulations. Unlike the two immunodominant public TCRs crystallized so far, which focused on one peptide hotspot, the HCMV-specific RA14 TCR interacts with the full array of available peptide residues. The conservation of some peptide-MHC complex-contacting amino acids by lower-affinity TCRs suggests a shared TCR-peptide-MHC complex docking mode and supports an Ag-driven selection of optimal TCRs. Therefore, the emergence of a public TCR of an oligoclonal Ag-specific response after repeated viral stimulations is based on a receptor displaying a high structural complementarity with the entire peptide and focusing on three peptide hotspots. This highlights key parameters underlying the selection of a protective T cell response against HCMV infection, which remains a major health issue in patients undergoing bone marrow transplantation.


  • Organizational Affiliation

    Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS, UJF, PSB, Grenoble, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chainA [auth H]274Homo sapiensMutation(s): 1 
Gene Names: HLAHLA-AHLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens)
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Go to UniProtKB:  P04439
PHAROS:  P04439
GTEx:  ENSG00000206503 
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UniProt GroupP04439
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HCMV pp65 fragment 495-503 (NLVPMVATV)B [auth P]9N/AMutation(s): 0 
Sequence Annotations
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulinC [auth L]100Homo sapiensMutation(s): 0 
Gene Names: B2MBeta-2 microglubulinCDABP0092HDCMA22P
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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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RA14 TCR alpha chain (TRAV24, TRAJ49)D [auth A]199Homo sapiensMutation(s): 0 
Gene Names: TCR
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Find proteins for P01848 (Homo sapiens)
Explore P01848 
Go to UniProtKB:  P01848
PHAROS:  P01848
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UniProt GroupP01848
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RA14 TCR beta chain (TRBV6-5, TRBD1, TRBJ1-2)E [auth B]243Homo sapiensMutation(s): 0 
Gene Names: TCR
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.237 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.45α = 90
b = 77.06β = 101.95
c = 87.22γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations