7X00

Crystal structure of peptide VSFIEFVGW in complex with HLA-B5801


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.144 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Allopurinol non-covalently facilitates binding of unconventional peptides to HLA-B*58:01.

Huan, X.Zhuo, N.Lee, H.Y.Ren, E.C.

(2023) Sci Rep 13: 9373-9373

  • DOI: https://doi.org/10.1038/s41598-023-36293-z
  • Primary Citation of Related Structures:  
    7WZZ, 7X00, 7X1B, 7X1C

  • PubMed Abstract: 

    Allopurinol, widely used in gout treatment, is the most common cause of severe cutaneous adverse drug reactions. The risk of developing such life-threatening reactions is increased particularly for HLA-B*58:01 positive individuals. However the mechanism of action between allopurinol and HLA remains unknown. We demonstrate here that a Lamin A/C peptide KAGQVVTI which is unable to bind HLA-B*58:01 on its own, is enabled to form a stable peptide-HLA complex only in the presence of allopurinol. Crystal structure analysis reveal that allopurinol non-covalently facilitated KAGQVVTI to adopt an unusual binding conformation, whereby the C-terminal isoleucine does not engage as a PΩ that typically fit deeply in the binding F-pocket. A similar observation, though to a lesser degree was seen with oxypurinol. Presentation of unconventional peptides by HLA-B*58:01 aided by allopurinol contributes to our fundamental understanding of drug-HLA interactions. The binding of peptides from endogenously available proteins such as self-protein lamin A/C and viral protein EBNA3B suggest that aberrant loading of unconventional peptides in the presence of allopurinol or oxypurinol may be able to trigger anti-self reactions that can lead to Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN) and Drug Reaction with Eosinophilia and Systemic Symptoms (DRESS).


  • Organizational Affiliation

    Singapore Immunology Network (SigN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos, Singapore, 138648, Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I antigen277Homo sapiensMutation(s): 0 
Gene Names: HLA-B
UniProt
Find proteins for F4NC28 (Homo sapiens)
Explore F4NC28 
Go to UniProtKB:  F4NC28
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF4NC28
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Homo sapiensMutation(s): 0 
Gene Names: B2M
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
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VAL-SER-PHE-ILE-GLU-PHE-VAL-GLY-TRP9synthetic constructMutation(s): 0 
UniProt
Find proteins for P03203 (Epstein-Barr virus (strain B95-8))
Explore P03203 
Go to UniProtKB:  P03203
Entity Groups  
UniProt GroupP03203
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.715α = 90
b = 82.055β = 90
c = 110.277γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentSingaporeF00006

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-03
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2023-10-25
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Refinement description