1H15

X-ray crystal structure of HLA-DRA1*0101/DRB5*0101 complexed with a peptide from Epstein Barr Virus DNA polymerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.256 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Functional and Structural Basis for Tcr Cross-Reactivity in Multiple Sclerosis

Lang, H.Jacobsen, H.Ikemizu, S.Andersson, C.Harlos, K.Madsen, L.Hjorth, P.Sondergaard, L.Svejgaard, A.Wucherpfennig, K.Stuart, D.I.Bell, J.I.Jones, E.Y.Fugger, L.

(2002) Nat Immunol 3: 940

  • DOI: 10.1038/ni835
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The multiple sclerosis (MS)-associated HLA major histocompatibility complex (MHC) class II alleles DRB1*1501, DRB5*0101 and DQB1*0602 are in strong linkage disequilibrium, making it difficult to determine which is the principal MS risk gene. Here we ...

    The multiple sclerosis (MS)-associated HLA major histocompatibility complex (MHC) class II alleles DRB1*1501, DRB5*0101 and DQB1*0602 are in strong linkage disequilibrium, making it difficult to determine which is the principal MS risk gene. Here we show that together the DRB1 and DRB5 loci may influence susceptibility to MS. We demonstrate that a T cell receptor (TCR) from an MS patient recognized both a DRB1*1501-restricted myelin basic protein (MBP) and DRB5*0101-restricted Epstein-Barr virus (EBV) peptide. Crystal structure determination of the DRB5*0101-EBV peptide complex revealed a marked degree of structural equivalence to the DRB1*1501-MBP peptide complex at the surface presented for TCR recognition. This provides structural evidence for molecular mimicry involving HLA molecules. The structural details suggest an explanation for the preponderance of MHC class II associations in HLA-associated diseases.


    Organizational Affiliation

    Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
A, D
182Homo sapiensMutation(s): 0 
Gene Names: HLA-DRAHLA-DRA1
Find proteins for P01903 (Homo sapiens)
Go to UniProtKB:  P01903
NIH Common Fund Data Resources
PHAROS  P01903

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR BETA 1 CHAIN
B, E
190Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB5
Find proteins for Q30154 (Homo sapiens)
Go to UniProtKB:  Q30154
NIH Common Fund Data Resources
PHAROS  Q30154
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA POLYMERASE
C, F
14Human gammaherpesvirus 4Mutation(s): 0 
EC: 2.7.7.7
Find proteins for P03198 (Epstein-Barr virus (strain B95-8))
Go to UniProtKB:  P03198
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.256 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 179.244α = 90
b = 179.244β = 90
c = 92.884γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-03
    Type: Initial release
  • Version 1.1: 2011-09-28
    Changes: Advisory, Atomic model, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
  • Version 1.2: 2012-06-27
    Changes: Other