6XQQ

Structure of human D462-E4 TCR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Atypical TRAV1-2 - T cell receptor recognition of the antigen-presenting molecule MR1.

Awad, W.Meermeier, E.W.Sandoval-Romero, M.L.Le Nours, J.Worley, A.H.Null, M.D.Liu, L.McCluskey, J.Fairlie, D.P.Lewinsohn, D.M.Rossjohn, J.

(2020) J Biol Chem 295: 14445-14457

  • DOI: 10.1074/jbc.RA120.015292
  • Primary Citation of Related Structures:  
    6XQP, 6XQQ

  • PubMed Abstract: 
  • MR1 presents vitamin B-related metabolites to mucosal associated invariant T (MAIT) cells, which are characterized, in part, by the TRAV1-2 + αβ T cell receptor (TCR). In addition, a more diverse TRAV1-2 - MR1-restricted T cel ...

    MR1 presents vitamin B-related metabolites to mucosal associated invariant T (MAIT) cells, which are characterized, in part, by the TRAV1-2 + αβ T cell receptor (TCR). In addition, a more diverse TRAV1-2 - MR1-restricted T cell repertoire exists that can possess altered specificity for MR1 antigens. However, the molecular basis of how such TRAV1-2 - TCRs interact with MR1-antigen complexes remains unclear. Here, we describe how a TRAV12-2 + TCR (termed D462-E4) recognizes an MR1-antigen complex. We report the crystal structures of the unliganded D462-E4 TCR and its complex with MR1 presenting the riboflavin-based antigen 5-OP-RU. Here, the TRBV29-1 β-chain of the D462-E4 TCR binds over the F'-pocket of MR1, whereby the complementarity-determining region (CDR) 3β loop surrounded and projected into the F'-pocket. Nevertheless, the CDR3β loop anchored proximal to the MR1 A'-pocket and mediated direct contact with the 5-OP-RU antigen. The D462-E4 TCR footprint on MR1 contrasted that of the TRAV1-2 + and TRAV36 + TCRs' docking topologies on MR1. Accordingly, diverse MR1-restricted T cell repertoire reveals differential docking modalities on MR1, thus providing greater scope for differing antigen specificities.


    Organizational Affiliation

    Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRAV12-2 alpha chainAC205Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TRBV29-1BD248Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.222α = 90
b = 115.222β = 90
c = 183.992γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-07-10 
  • Released Date: 2020-08-19 
  • Deposition Author(s): Awad, W., Rossjohn, J.

Funding OrganizationLocationGrant Number
Australian Research Council (ARC)Australia--

Revision History 

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2020-09-02
    Changes: Database references
  • Version 1.2: 2020-10-28
    Changes: Database references