4GRL

Crystal structure of a autoimmune TCR-MHC complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 
    0.256 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

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Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

Crossreactivity of a human autoimmune TCR is dominated by a single TCR loop.

Sethi, D.K.Gordo, S.Schubert, D.A.Wucherpfennig, K.W.

(2013) Nat Commun 4: 2623-2623

  • DOI: https://doi.org/10.1038/ncomms3623
  • Primary Citation of Related Structures:  
    4GRL, 4MAY

  • PubMed Abstract: 

    Self-reactive CD4 T cells are thought to have a central role in the pathogenesis of many chronic inflammatory human diseases. Microbial peptides can activate self-reactive T cells, but the structural basis for such crossreactivity is not well understood. The Hy.1B11 T cell receptor (TCR) originates from a patient with multiple sclerosis and recognizes the self-antigen myelin basic protein. Here we report the structural mechanism of TCR crossreactivity with two distinct peptides from human pathogens. The structures show that a single TCR residue (CDR3α F95) makes the majority of contacts with the self-peptide and both microbial peptides (66.7-80.6%) due to a highly tilted TCR-binding topology on the peptide-MHC surface. Further, a neighbouring residue located on the same TCR loop (CDR3α E98) forms an energetically critical interaction with the MHC molecule. These data show how binding by a self-reactive TCR favors crossreactivity between self and microbial antigens.


  • Organizational Affiliation

    Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class II HLA-DQ-alpha chain183Homo sapiensMutation(s): 0 
Gene Names: alpha chainHLA-DQ1HLA-DQA1MHC CLASS II MOLECULE
UniProt
Find proteins for Q30066 (Homo sapiens)
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Go to UniProtKB:  Q30066
Entity Groups  
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UniProt GroupQ30066
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class II antigen200Homo sapiensMutation(s): 0 
Gene Names: beta chainHLA-DQ1HLA-DQB1MHC CLASS II MOLECULE
UniProt
Find proteins for Q67AJ6 (Homo sapiens)
Explore Q67AJ6 
Go to UniProtKB:  Q67AJ6
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UniProt GroupQ67AJ6
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
TCR Hy.1B11 alpha chain209Homo sapiensMutation(s): 0 
Gene Names: TCR Hy.1B11 alpha chain
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
TCR Hy.1B11 beta chain268Homo sapiensMutation(s): 0 
Gene Names: TCR Hy.1B11 beta chain
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Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free:  0.256 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.011α = 90
b = 125.583β = 90
c = 134.794γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Structure summary