4D8P

Structural and functional studies of the trans-encoded HLA-DQ2.3 (DQA1*03:01/DQB1*02:01) molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural and functional studies of trans-encoded HLA-DQ2.3 (DQA1*03:01/DQB1*02:01) protein molecule

Tollefsen, S.Hotta, K.Chen, X.Simonsen, B.Swaminathan, K.Mathews, I.I.Sollid, L.M.Kim, C.-Y.

(2012) J Biol Chem 287: 13611-13619

  • DOI: https://doi.org/10.1074/jbc.M111.320374
  • Primary Citation of Related Structures:  
    4D8P

  • PubMed Abstract: 

    MHC class II molecules are composed of one α-chain and one β-chain whose membrane distal interface forms the peptide binding groove. Most of the existing knowledge on MHC class II molecules comes from the cis-encoded variants where the α- and β-chain are encoded on the same chromosome. However, trans-encoded class II MHC molecules, where the α- and β-chain are encoded on opposite chromosomes, can also be expressed. We have studied the trans-encoded class II HLA molecule DQ2.3 (DQA1*03:01/DQB1*02:01) that has received particular attention as it may explain the increased risk of certain individuals to type 1 diabetes. We report the x-ray crystal structure of this HLA molecule complexed with a gluten epitope at 3.05 Å resolution. The gluten epitope, which is the only known HLA-DQ2.3-restricted epitope, is preferentially recognized in the context of the DQ2.3 molecule by T-cell clones of a DQ8/DQ2.5 heterozygous celiac disease patient. This preferential recognition can be explained by improved HLA binding as the epitope combines the peptide-binding motif of DQ2.5 (negative charge at P4) and DQ8 (negative charge at P1). The analysis of the structure of DQ2.3 together with all other available DQ crystal structures and sequences led us to categorize DQA1 and DQB1 genes into two groups where any α-chain and β-chain belonging to the same group are expected to form a stable heterodimer.


  • Organizational Affiliation

    Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, Rikshospitalet, 0027 Oslo, Norway.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA-DQA1 protein
A, C
213Homo sapiensMutation(s): 0 
Gene Names: HLA-DQA1
UniProt
Find proteins for L8E864 (Homo sapiens)
Explore L8E864 
Go to UniProtKB:  L8E864
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL8E864
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide from Gamma-gliadin,HLA class II histocompatibility antigen, DQ beta 1 chain
B, D
250Triticum aestivumHomo sapiens
This entity is chimeric
Mutation(s): 2 
UniProt
Find proteins for Q94G94 (Triticum aestivum)
Explore Q94G94 
Go to UniProtKB:  Q94G94
Find proteins for Q5Y7D3 (Homo sapiens)
Explore Q5Y7D3 
Go to UniProtKB:  Q5Y7D3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ94G94Q5Y7D3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.89α = 90
b = 114.92β = 103.36
c = 138.03γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2014-03-12
    Changes: Database references
  • Version 1.2: 2017-06-21
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description