7ZT5

Structure of E8 TCR in complex in human MR1 bound to 3FSA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Promiscuous recognition of MR1 drives self-reactive mucosal-associated invariant T cell responses.

Chancellor, A.Alan Simmons, R.Khanolkar, R.C.Nosi, V.Beshirova, A.Berloffa, G.Colombo, R.Karuppiah, V.Pentier, J.M.Tubb, V.Ghadbane, H.Suckling, R.J.Page, K.Crean, R.M.Vacchini, A.De Gregorio, C.Schaefer, V.Constantin, D.Gligoris, T.Lloyd, A.Hock, M.Srikannathasan, V.Robinson, R.A.Besra, G.S.van der Kamp, M.W.Mori, L.Calogero, R.Cole, D.K.De Libero, G.Lepore, M.

(2023) J Exp Med 220

  • DOI: https://doi.org/10.1084/jem.20221939
  • Primary Citation of Related Structures:  
    7ZT2, 7ZT3, 7ZT4, 7ZT5, 7ZT7, 7ZT8, 7ZT9

  • PubMed Abstract: 

    Mucosal-associated invariant T (MAIT) cells use canonical semi-invariant T cell receptors (TCR) to recognize microbial riboflavin precursors displayed by the antigen-presenting molecule MR1. The extent of MAIT TCR crossreactivity toward physiological, microbially unrelated antigens remains underexplored. We describe MAIT TCRs endowed with MR1-dependent reactivity to tumor and healthy cells in the absence of microbial metabolites. MAIT cells bearing TCRs crossreactive toward self are rare but commonly found within healthy donors and display T-helper-like functions in vitro. Experiments with MR1-tetramers loaded with distinct ligands revealed significant crossreactivity among MAIT TCRs both ex vivo and upon in vitro expansion. A canonical MAIT TCR was selected on the basis of extremely promiscuous MR1 recognition. Structural and molecular dynamic analyses associated promiscuity to unique TCRβ-chain features that were enriched within self-reactive MAIT cells of healthy individuals. Thus, self-reactive recognition of MR1 represents a functionally relevant indication of MAIT TCR crossreactivity, suggesting a potentially broader role of MAIT cells in immune homeostasis and diseases, beyond microbial immunosurveillance.


  • Organizational Affiliation

    Experimental Immunology, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major histocompatibility complex class I-related gene protein290Homo sapiensMutation(s): 0 
Gene Names: MR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q95460 (Homo sapiens)
Explore Q95460 
Go to UniProtKB:  Q95460
PHAROS:  Q95460
GTEx:  ENSG00000153029 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ95460
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
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
TCR alphaC [auth D]205Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
TCR betaD [auth E]262Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7ZS (Subject of Investigation/LOI)
Query on 7ZS

Download Ideal Coordinates CCD File 
E [auth A]3-methanoyl-2-oxidanyl-benzoic acid
C8 H6 O4
YOEUNKPREOJHBW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.97α = 90
b = 104.67β = 90
c = 117.7γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release
  • Version 1.1: 2023-07-12
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary