3VRJ

HLA-B*57:01-LTTKLTNTNI in complex with abacavir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Immune self-reactivity triggered by drug-modified HLA-peptide repertoire

Illing, P.T.Vivian, J.P.Dudek, N.L.Kostenko, L.Chen, Z.Bharadwaj, M.Miles, J.J.Kjer-Nielsen, L.Gras, S.Williamson, N.A.Burrows, S.R.Purcell, A.W.Rossjohn, J.McCluskey, J.

(2012) Nature 486: 554-558

  • DOI: 10.1038/nature11147
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human leukocyte antigens (HLAs) are highly polymorphic proteins that initiate immunity by presenting pathogen-derived peptides to T cells. HLA polymorphisms mostly map to the antigen-binding cleft, thereby diversifying the repertoire of self-derived ...

    Human leukocyte antigens (HLAs) are highly polymorphic proteins that initiate immunity by presenting pathogen-derived peptides to T cells. HLA polymorphisms mostly map to the antigen-binding cleft, thereby diversifying the repertoire of self-derived and pathogen-derived peptide antigens selected by different HLA allotypes. A growing number of immunologically based drug reactions, including abacavir hypersensitivity syndrome (AHS) and carbamazepine-induced Stevens-Johnson syndrome (SJS), are associated with specific HLA alleles. However, little is known about the underlying mechanisms of these associations, including AHS, a prototypical HLA-associated drug reaction occurring exclusively in individuals with the common histocompatibility allele HLA-B*57:01, and with a relative risk of more than 1,000 (refs 6, 7). We show that unmodified abacavir binds non-covalently to HLA-B*57:01, lying across the bottom of the antigen-binding cleft and reaching into the F-pocket, where a carboxy-terminal tryptophan typically anchors peptides bound to HLA-B*57:01. Abacavir binds with exquisite specificity to HLA-B*57:01, changing the shape and chemistry of the antigen-binding cleft, thereby altering the repertoire of endogenous peptides that can bind HLA-B*57:01. In this way, abacavir guides the selection of new endogenous peptides, inducing a marked alteration in 'immunological self'. The resultant peptide-centric 'altered self' activates abacavir-specific T-cells, thereby driving polyclonal CD8 T-cell activation and a systemic reaction manifesting as AHS. We also show that carbamazepine, a widely used anti-epileptic drug associated with hypersensitivity reactions in HLA-B*15:02 individuals, binds to this allotype, producing alterations in the repertoire of presented self peptides. Our findings simultaneously highlight the importance of HLA polymorphism in the evolution of pharmacogenomics and provide a general mechanism for some of the growing number of HLA-linked hypersensitivities that involve small-molecule drugs.


    Organizational Affiliation

    Department of Microbiology & Immunology, University of Melbourne, Parkville, Victoria 3010, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, B-57 alpha chain
A
276Homo sapiensMutation(s): 0 
Gene Names: HLA-B (HLAB)
Find proteins for P18465 (Homo sapiens)
Go to Gene View: HLA-B
Go to UniProtKB:  P18465
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
100Homo 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
10-mer peptide
C
10Homo sapiensMutation(s): 0 
Gene Names: MT-CO2 (COII, COX2, COXII, MTCO2)
Find proteins for P00403 (Homo sapiens)
Go to Gene View: MT-CO2
Go to UniProtKB:  P00403
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1KX
Query on 1KX

Download SDF File 
Download CCD File 
A
{(1S,4R)-4-[2-amino-6-(cyclopropylamino)-9H-purin-9-yl]cyclopent-2-en-1-yl}methanol
Abacavir
C14 H18 N6 O
MCGSCOLBFJQGHM-SCZZXKLOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.291α = 90.00
b = 49.005β = 99.53
c = 70.875γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
Blu-Icedata collection
SCALAdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2012-07-04
    Type: Database references