2YPL

Structural features underlying T-cell receptor sensitivity to concealed MHC class I micropolymorphisms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Features Underlying T-Cell Receptor Sensitivity to Concealed Mhc Class I Micropolymorphisms.

Stewart-Jones, G.B.Simpson, P.Anton Van Der Merwe, P.Easterbrook, P.Mcmichael, A.J.Rowland-Jones, S.L.Jones, E.Y.Gillespie, G.M.

(2012) Proc Natl Acad Sci U S A 109: E3483

  • DOI: https://doi.org/10.1073/pnas.1207896109
  • Primary Citation of Related Structures:  
    2YPK, 2YPL

  • PubMed Abstract: 

    Polymorphic differences distinguishing MHC class I subtypes often permit the presentation of shared epitopes in conformationally identical formats but can affect T-cell repertoire selection, differentially impacting autoimmune susceptibilities and viral clearance in vivo. The molecular mechanisms underlying this effect are not well understood. We performed structural, thermodynamic, and functional analyses of a conserved T-cell receptor (TCR) which is frequently expanded in response to a HIV-1 epitope when presented by HLA-B*5701 but is not selected by HLA-B*5703, which differs from HLA-B*5701 by two concealed polymorphisms. Our findings illustrate that although both HLA-B*57 subtypes display the epitope in structurally conserved formats, the impact of their polymorphic differences occurs directly as a consequence of TCR ligation, primarily because of peptide adjustments required for TCR binding, which involves the interplay of polymorphic residues and water molecules. These minor differences culminate in subtype-specific differential TCR-binding kinetics and cellular function. Our data demonstrate a potential mechanism whereby the most subtle MHC class I micropolymorphisms can influence TCR use and highlight their implications for disease outcomes.


  • Organizational Affiliation

    Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, United Kingdom.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-57 ALPHA CHAIN274Homo 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 
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UniProt GroupP01889
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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 
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UniProt GroupP61769
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
KF11 P24 GAG PEPTIDE11Human immunodeficiency virusMutation(s): 0 
UniProt
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Go to UniProtKB:  Q70XD7
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UniProt GroupQ70XD7
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
AGA T-CELL RECEPTOR ALPHA CHAIN199Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
AGA T-CELL RECEPTOR BETA CHAIN238Homo sapiensMutation(s): 0 
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.348α = 90
b = 75.605β = 90
c = 241.527γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-28
    Type: Initial release
  • Version 1.1: 2012-12-19
    Changes: Database references
  • Version 1.2: 2013-01-16
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description
  • Version 1.4: 2024-11-06
    Changes: Structure summary