2CIK | pdb_00002cik

Insights Into Crossreactivity in Human Allorecognition: The Structure of HLA-B35011 Presenting an Epitope derived from Cytochrome P450.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.227 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history

Literature

The Structure of the Human Allo-Ligand Hla-B3501 in Complex with a Cytochrome P450 Peptide: Steric Hindrance Influences Tcr Allo-Recognition.

Hourigan, C.S.Harkiolaki, M.Peterson, N.A.Bell, J.I.Jones, E.Y.O'Callaghan, C.A.

(2006) Eur J Immunol 36: 3288

  • DOI: https://doi.org/10.1002/eji.200636234
  • Primary Citation Related Structures: 
    2CIK

  • PubMed Abstract: 

    Virus-specific T cell populations have been implicated in allo-recognition. The subdominant T cell receptor JL12 recognizes both HLA-B*0801 presenting the Epstein-Barr virus-derived peptide FLRGRAYGL and also HLA-B*3501 presenting the cytochrome p450 self peptide KPIVVLHGY. This cross-reactivity could promote the rejection of HLA-B*3501-positive cells in Epstein-Barr virus-exposed HLA-B*0801 recipients. LC13, the dominant TCR against the HLA-B*0801:FLRGRAYGL complex, fails to recognize HLA-B*3501:KPIVVLHGY. We report the 1.75-Angstrom resolution crystal structure of the human allo-ligand HLA-B*3501:KPIVVLHGY. Similarities between this structure and that of HLA-B*0801:FLRGRAYGL may facilitate cross-recognition by JL12. Moreover, the elevated peptide position in HLA-B*3501:KPIVVLHGY would provide steric hindrance to LC13, preventing it from interacting in the manner in which it interacts with HLA-B*0801:FLRGRAYGL. These findings are relevant to understanding the basis of T cell cross-reactivity in allo-recognition, optimal transplant donor-recipient matching and developing specific molecular inhibitors of allo-recognition.


  • Organizational Affiliation
    • Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, UK.

Macromolecule Content 

  • Total Structure Weight: 44.99 kDa 
  • Atom Count: 3,499 
  • Modeled Residue Count: 384 
  • Deposited Residue Count: 384 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA CLASS I HISTOCOMPATIBILITY ANTIGEN B-35 ALPHA CHAIN276Homo sapiensMutation(s): 0 
UniProt
Find proteins for O19626 (Homo sapiens)
Explore O19626 
Go to UniProtKB:  O19626
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO19626
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
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
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
PEPTIDE9Homo sapiensMutation(s): 0 
EC: 1.14.14.1
UniProt & NIH Common Fund Data Resources
Find proteins for P33260 (Homo sapiens)
Explore P33260 
Go to UniProtKB:  P33260
PHAROS:  P33260
GTEx:  ENSG00000108242 
Entity Groups
UniProt GroupP33260
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.227 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.32α = 90
b = 82.25β = 90
c = 109.85γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-25
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary