4PRH

Crystal structure of TK3 TCR-HLA-B*35:08-HPVG-D5 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Molecular Basis for the Interplay between T Cells, Viral Mutants, and Human Leukocyte Antigen Micropolymorphism.

Liu, Y.C.Chen, Z.Neller, M.A.Miles, J.J.Purcell, A.W.McCluskey, J.Burrows, S.R.Rossjohn, J.Gras, S.

(2014) J.Biol.Chem. 289: 16688-16698

  • DOI: 10.1074/jbc.M114.563502
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mutations within T cell epitopes represent a common mechanism of viral escape from the host protective immune response. The diverse T cell repertoire and the extensive human leukocyte antigen (HLA) polymorphism across populations is the evolutionary ...

    Mutations within T cell epitopes represent a common mechanism of viral escape from the host protective immune response. The diverse T cell repertoire and the extensive human leukocyte antigen (HLA) polymorphism across populations is the evolutionary response to viral mutation. However, the molecular basis underpinning the interplay between HLA polymorphism, the T cell repertoire, and viral escape is unclear. Here we investigate the T cell response to a HLA-B*35:01- and HLA-B*35:08-restricted (407)HPVGEADYFEY(417) epitope from Epstein-Barr virus and naturally occurring variants at positions 4 and 5 thereof. Each viral variant differently impacted on the epitope's flexibility and conformation when bound to HLA-B*35:08 or HLA-B*35:01. We provide a molecular basis for understanding how the single residue polymorphism that discriminates between HLA-B*35:01/08 profoundly impacts on T cell receptor recognition. Surprisingly, one viral variant (P5-Glu to P5-Asp) effectively changed restriction preference from HLA-B*35:01 to HLA-B*35:08. Collectively, our study portrays the interplay between the T cell response, viral escape, and HLA polymorphism, whereby HLA polymorphism enables altered presentation of epitopes from different strains of Epstein-Barr virus.


    Organizational Affiliation

    From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Melbourne 3800, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MHC class I antigen
A
272Homo sapiensMutation(s): 0 
Gene Names: HLA-B
Find proteins for C5MK56 (Homo sapiens)
Go to Gene View: HLA-B
Go to UniProtKB:  C5MK56
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
100Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Epstein-Barr nuclear antigen 1
C
11Epstein-Barr virus (strain GD1)Mutation(s): 0 
Gene Names: EBNA1
Find proteins for Q3KSS4 (Epstein-Barr virus (strain GD1))
Go to UniProtKB:  Q3KSS4
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
TK3 TCR alpha chain
D
208Homo sapiensMutation(s): 0 
Gene Names: TRAC (TCRA)
Find proteins for P01848 (Homo sapiens)
Go to UniProtKB:  P01848
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
TK3 TCR beta chain
E
243Homo sapiensMutation(s): 0 
Gene Names: TRBC1
Find proteins for P01850 (Homo sapiens)
Go to UniProtKB:  P01850
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.212 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 44.835α = 92.70
b = 62.081β = 101.92
c = 98.334γ = 108.21
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XSCALEdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-30
    Type: Initial release
  • Version 1.1: 2014-06-18
    Type: Database references
  • Version 1.2: 2014-07-02
    Type: Database references