1M6O

Crystal Structure of HLA B*4402 in complex with HLA DPA*0201 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A naturally selected dimorphism within the HLA-B44 supertype alters class I structure, peptide repertoire, and T cell recognition.

Macdonald, W.A.Purcell, A.W.Mifsud, N.A.Ely, L.K.Williams, D.S.Chang, L.Gorman, J.J.Clements, C.S.Kjer-Nielsen, L.Koelle, D.M.Burrows, S.R.Tait, B.D.Holdsworth, R.Brooks, A.G.Lovrecz, G.O.Lu, L.Rossjohn, J.McCluskey, J.

(2003) J Exp Med 198: 679-691

  • DOI: https://doi.org/10.1084/jem.20030066
  • Primary Citation of Related Structures:  
    1M6O, 1N2R

  • PubMed Abstract: 

    HLA-B*4402 and B*4403 are naturally occurring MHC class I alleles that are both found at a high frequency in all human populations, and yet they only differ by one residue on the alpha2 helix (B*4402 Asp156-->B*4403 Leu156). CTLs discriminate between HLA-B*4402 and B*4403, and these allotypes stimulate strong mutual allogeneic responses reflecting their known barrier to hemopoeitic stem cell transplantation. Although HLA-B*4402 and B*4403 share >95% of their peptide repertoire, B*4403 presents more unique peptides than B*4402, consistent with the stronger T cell alloreactivity observed toward B*4403 compared with B*4402. Crystal structures of B*4402 and B*4403 show how the polymorphism at position 156 is completely buried and yet alters both the peptide and the heavy chain conformation, relaxing ligand selection by B*4403 compared with B*4402. Thus, the polymorphism between HLA-B*4402 and B*4403 modifies both peptide repertoire and T cell recognition, and is reflected in the paradoxically powerful alloreactivity that occurs across this "minimal" mismatch. The findings suggest that these closely related class I genes are maintained in diverse human populations through their differential impact on the selection of peptide ligands and the T cell repertoire.


  • Organizational Affiliation

    Dept. of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria 3010, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, BW-44(B-12) B*4402 alpha chain276Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens)
Explore P01889 
Go to UniProtKB:  P01889
PHAROS:  P01889
GTEx:  ENSG00000234745 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01889
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HLA DPA*0201 peptide9N/AMutation(s): 0 
UniProt
Find proteins for Q95HB9 (Homo sapiens)
Explore Q95HB9 
Go to UniProtKB:  Q95HB9
Entity Groups  
UniProt GroupQ95HB9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.805α = 90
b = 81.781β = 90
c = 110.069γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
d*TREKdata reduction
AMoREphasing
CNSrefinement
HKL-2000data reduction
d*TREKdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-02
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance