Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 91.12 kDa 
• Atom Count: 6420 
• Modelled Residue Count: 766 
• Deposited Residue Count: 772 
• Unique protein chains: 3

1H15

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

• PDB DOI: 10.2210/pdb1H15/pdb

• Classification: IMMUNE SYSTEM/TRANSFERASE
• Organism(s): Homo sapiens, Human gammaherpesvirus 4
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2002-07-02 Released: 2002-10-03 
• Deposition Author(s): 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.

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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 

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

• PubMed: 12244309 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN	A, D	182	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRA, HLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens) Explore P01903  Go to UniProtKB:  P01903
PHAROS:  P01903 GTEx:  ENSG00000204287

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR BETA 1 CHAIN	B, E	190	Homo sapiens	Mutation(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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA POLYMERASE	C, F	14	Human gammaherpesvirus 4	Mutation(s): 0  EC: 2.7.7.7
UniProt
Find proteins for P03198 (Epstein-Barr virus (strain B95-8)) Explore P03198  Go to UniProtKB:  P03198

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	H [auth A], I [auth D], J [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

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 = 179.244	α = 90
b = 179.244	β = 90
c = 92.884	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-07-02 
• Released Date: 2002-10-03 
Deposition Author(s): 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.

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