4LCC

Crystal structure of a human MAIT TCR in complex with a bacterial antigen bound to humanized bovine MR1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.263 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

MAIT Recognition of a Stimulatory Bacterial Antigen Bound to MR1.

Lopez-Sagaseta, J.Dulberger, C.L.McFedries, A.Cushman, M.Saghatelian, A.Adams, E.J.

(2013) J.Immunol. 191: 5268-5277

  • DOI: 10.4049/jimmunol.1301958
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • MR1-restricted mucosal-associated invariant T (MAIT) cells represent a subpopulation of αβ T cells with innate-like properties and limited TCR diversity. MAIT cells are of interest because of their reactivity against bacterial and yeast species, sugg ...

    MR1-restricted mucosal-associated invariant T (MAIT) cells represent a subpopulation of αβ T cells with innate-like properties and limited TCR diversity. MAIT cells are of interest because of their reactivity against bacterial and yeast species, suggesting that they play a role in defense against pathogenic microbes. Despite the advances in understanding MAIT cell biology, the molecular and structural basis behind their ability to detect MR1-Ag complexes is unclear. In this study, we present our structural and biochemical characterization of MAIT TCR engagement of MR1 presenting an Escherichia coli-derived stimulatory ligand, rRL-6-CH2OH, previously found in Salmonella typhimurium. We show a clear enhancement of MAIT TCR binding to MR1 due to the presentation of this ligand. Our structure of a MAIT TCR/MR1/rRL-6-CH2OH complex shows an evolutionarily conserved binding orientation, with a clear role for both the CDR3α and CDR3β loops in recognizing the rRL-6-CH2OH stimulatory ligand. We also present two additional xenoreactive MAIT TCR/MR1 complexes that recapitulate the docking orientation documented previously, despite having variation in the CDR2β and CDR3β loop sequences. Our data support a model by which MAIT TCRs engage MR1 in a conserved fashion, with their binding affinities modulated by the nature of the MR1-presented Ag or diversity introduced by alternate Vβ usage or CDR3β sequences.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin, MHC class I-related protein
C
392Bos taurusMutation(s): 3 
Gene Names: MR1, B2M
Find proteins for C1ITJ8 (Bos taurus)
Go to Gene View: MR1
Go to UniProtKB:  C1ITJ8
Find proteins for P01888 (Bos taurus)
Go to Gene View: B2M
Go to UniProtKB:  P01888
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Human MAIT TCR alpha chain
A
208Homo sapiensMutation(s): 0 
Gene Names: TRA@
Find proteins for Q6P4G7 (Homo sapiens)
Go to UniProtKB:  Q6P4G7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Human MAIT TCR beta chain
B
253Homo sapiensMutation(s): 0 
Gene Names: TRBC1
Find proteins for P01850 (Homo sapiens)
Go to UniProtKB:  P01850
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
1XL
Query on 1XL

Download SDF File 
Download CCD File 
C
1-deoxy-1-[6-(hydroxymethyl)-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl]-D-arabinitol
C12 H16 N4 O7
RTNMDIMJQSRAGT-BHNWBGBOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.263 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.257 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 85.902α = 90.00
b = 88.585β = 90.00
c = 155.505γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2013-11-20
    Type: Database references
  • Version 1.2: 2017-08-23
    Type: Refinement description, Source and taxonomy
  • Version 1.3: 2018-01-24
    Type: Structure summary