1N2R

A natural selected dimorphism in HLA B*44 alters self, peptide reportoire and T cell recognition.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.229 

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: 10.1084/jem.20030066
  • Primary Citation of Related Structures:  

  • 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 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, BW-44(B-12) B*4403 alpha chain
A
276Homo sapiensMutation(s): 0 
Gene Names: HLA-B (HLAB)
Find proteins for P30481 (Homo sapiens)
Go to Gene View: HLA-B
Go to UniProtKB:  P30481
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
99Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HLA DPA*0201 PEPTIDE
C
9Homo sapiensMutation(s): 0 
Gene Names: HLA-DPA1
Find proteins for Q95HB9 (Homo sapiens)
Go to Gene View: HLA-DPA1
Go to UniProtKB:  Q95HB9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACY
Query on ACY

Download SDF File 
Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.720α = 90.00
b = 82.295β = 90.00
c = 109.550γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-16
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance