1MI5

The crystal structure of LC13 TcR in complex with HLAB8-EBV peptide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A Structural Basis for the Selection of Dominant alphabeta T Cell Receptors in Antiviral Immunity

Kjer-Nielsen, L.Clements, C.S.Purcell, A.W.Brooks, A.G.Whisstock, J.C.Burrows, S.R.McCluskey, J.Rossjohn, J.

(2003) Immunity 18: 53-64

  • DOI: https://doi.org/10.1016/s1074-7613(02)00513-7
  • Primary Citation of Related Structures:  
    1MI5

  • PubMed Abstract: 

    We have examined the basis for immunodominant or "public" TCR usage in an antiviral CTL response. Residues encoded by each of the highly selected genetic elements of an immunodominant clonotype recognizing Epstein-Barr virus were critical to the antigen specificity of the receptor. Upon recognizing antigen, the immunodominant TCR undergoes extensive conformational changes in the complementarity determining regions (CDRs), including the disruption of the canonical structures of the germline-encoded CDR1alpha and CDR2alpha loops to produce an enhanced fit with the HLA-peptide complex. TCR ligation induces conformational changes in the TCRalpha constant domain thought to form part of the docking site for CD3epsilon. These findings indicate that TCR immunodominance is associated with structural properties conferring receptor specificity and suggest a novel structural link between TCR ligation and intracellular signaling.


  • Organizational Affiliation

    Department of Microbiology & Immunology, University of Melbourne, Parkville, Victoria 3010, Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC heavy chain277Homo sapiensMutation(s): 0 
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Find proteins for P01889 (Homo sapiens)
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PHAROS:  P01889
GTEx:  ENSG00000234745 
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UniProt GroupP01889
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
beta 2 microglobulin99Homo sapiensMutation(s): 0 
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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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Epstein Barr Virus peptide9N/AMutation(s): 0 
UniProt
Find proteins for Q3KST2 (Epstein-Barr virus (strain GD1))
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UniProt GroupQ3KST2
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
TcR alpha chain201Homo sapiensMutation(s): 0 
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Find proteins for P01848 (Homo sapiens)
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PHAROS:  P01848
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UniProt GroupP01848
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
TcR beta chain241Homo sapiensMutation(s): 0 
UniProt
Find proteins for P01850 (Homo sapiens)
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UniProt GroupP01850
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.49α = 90
b = 105.9β = 90
c = 144.5γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-04-03
    Changes: Data collection, Database references, Refinement description