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 

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Ligand Structure Quality Assessment 


This is version 2.0 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
  • Primary Citation of Related Structures:  
    1H15

  • 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 show that together the DRB1 and DRB5 loci may influence susceptibility to MS ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAINA, D182Homo sapiensMutation(s): 0 
Gene Names: HLA-DRAHLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens)
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Go to UniProtKB:  P01903
PHAROS:  P01903
GTEx:  ENSG00000204287 
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UniProt GroupP01903
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR BETA 1 CHAINB, E190Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB5
UniProt & NIH Common Fund Data Resources
Find proteins for Q30154 (Homo sapiens)
Explore Q30154 
Go to UniProtKB:  Q30154
PHAROS:  Q30154
GTEx:  ENSG00000198502 
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UniProt GroupQ30154
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA POLYMERASEC, F14Human gammaherpesvirus 4Mutation(s): 0 
EC: 2.7.7.7
UniProt
Find proteins for P03198 (Epstein-Barr virus (strain B95-8))
Explore P03198 
Go to UniProtKB:  P03198
Entity Groups  
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UniProt GroupP03198
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
H [auth A],
I [auth D],
J [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
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

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary