4PRB

Crystal structure of a HLA-B*35:08-HPVG-A4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.4 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.,QIMR Berghofer Medical Research Institute and QIMR Berghofer Centre for Immunotherapy and Vaccine Development, Brisbane, Queensland 4006, Australia.,From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Melbourne 3800, Australia, Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia stephanie.gras@monash.edu.,From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Melbourne 3800, Australia, Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN Wales, United Kingdom, and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia jamie.rossjohn@monash.edu.,Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MHC class I antigen
A
276Homo 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
99Homo 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 AG876)Mutation(s): 0 
Gene Names: EBNA1
Find proteins for Q1HVF7 (Epstein-Barr virus (strain AG876))
Go to UniProtKB:  Q1HVF7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.800α = 90.00
b = 82.100β = 90.00
c = 110.500γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
Blu-Icedata collection
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-04-23
    Type: Database references
  • Version 1.2: 2014-06-18
    Type: Database references
  • Version 1.3: 2014-07-02
    Type: Database references
  • Version 1.4: 2017-11-22
    Type: Refinement description