1M05

HLA B8 in complex with an Epstein Barr Virus determinant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The structure of HLA-B8 complexed to an immunodominant viral determinant: peptide-induced conformational changes and a mode of MHC class I dimerization.

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

(2003) J.IMMUNOL. 169: 5153-5160


  • PubMed Abstract: 
  • EBV is a ubiquitous human pathogen that chronically infects up to 90% of the population. Persistent viral infection is characterized by latency and periods of viral replication that are kept in check by a strong antiviral CTL response. Despite the si ...

    EBV is a ubiquitous human pathogen that chronically infects up to 90% of the population. Persistent viral infection is characterized by latency and periods of viral replication that are kept in check by a strong antiviral CTL response. Despite the size of the EBV genome, CTL immunity focuses on only a few viral determinants but expands a large primary and memory response toward these epitopes. In unrelated HLA-B8(+) individuals, the response to the immunodominant latent Ag FLRGRAYGL from Epstein Barr nuclear Ag 3A is largely comprised of CTL clones with identical conserved alphabeta TCR structures. To better understand the structural correlates of Ag immunodominance and TCR selection bias, we have solved the crystal structure of the HLA-B8-FLRGRAYGL peptide complex to a resolution of 1.9 A. The structure confirms the importance of P3-Arg, P5-Arg, and P9-Leu as dominant anchor residues involved in peptide binding to HLA-B8. A bulged conformation of the bound peptide provides a structural basis for the critical role of the P7-Tyr residue in T cell recognition. The peptide also induces backbone and side-chain conformational changes in HLA-B8 that are transmitted along the peptide-binding groove in a domino effect. The HLA-B8-FLRGRAYGL complex crystallizes as a dimer in the asymmetric unit and is oriented such that both peptide ligands are projected in the same plane suggesting a higher order arrangement of MHC-peptide complexes that could be involved in formation of the class I Ag-loading complex or in T cell activation.


    Organizational Affiliation

    Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, B-8 B*0801 alpha chain
A, C
277Homo sapiensGene Names: HLA-B (HLAB)
Find proteins for P30460 (Homo sapiens)
Go to Gene View: HLA-B
Go to UniProtKB:  P30460
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, D
99Homo sapiensGene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
EBNA-3 nuclear protein
E, F
9Epstein-Barr virus (strain B95-8)Gene Names: EBNA3
Find proteins for P12977 (Epstein-Barr virus (strain B95-8))
Go to UniProtKB:  P12977
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download SDF File 
Download CCD File 
B, D
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 85.400α = 90.00
b = 90.100β = 90.00
c = 125.300γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-02
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description