4L4V

Structure of human MAIT TCR in complex with human MR1-RL-6-Me-7-OH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Recognition of vitamin B metabolites by mucosal-associated invariant T cells.

Patel, O.Kjer-Nielsen, L.Le Nours, J.Eckle, S.B.Birkinshaw, R.Beddoe, T.Corbett, A.J.Liu, L.Miles, J.J.Meehan, B.Reantragoon, R.Sandoval-Romero, M.L.Sullivan, L.C.Brooks, A.G.Chen, Z.Fairlie, D.P.McCluskey, J.Rossjohn, J.

(2013) Nat Commun 4: 2142-2142

  • DOI: 10.1038/ncomms3142
  • Primary Citation of Related Structures:  4L4T

  • PubMed Abstract: 
  • The mucosal-associated invariant T-cell antigen receptor (MAIT TCR) recognizes MR1 presenting vitamin B metabolites. Here we describe the structures of a human MAIT TCR in complex with human MR1 presenting a non-stimulatory ligand derived from folic ...

    The mucosal-associated invariant T-cell antigen receptor (MAIT TCR) recognizes MR1 presenting vitamin B metabolites. Here we describe the structures of a human MAIT TCR in complex with human MR1 presenting a non-stimulatory ligand derived from folic acid and an agonist ligand derived from a riboflavin metabolite. For both vitamin B antigens, the MAIT TCR docks in a conserved manner above MR1, thus acting as an innate-like pattern recognition receptor. The invariant MAIT TCR α-chain usage is attributable to MR1-mediated interactions that prise open the MR1 cleft to allow contact with the vitamin B metabolite. Although the non-stimulatory antigen does not contact the MAIT TCR, the stimulatory antigen does. This results in a higher affinity of the MAIT TCR for a stimulatory antigen in comparison with a non-stimulatory antigen. We formally demonstrate a structural basis for MAIT TCR recognition of vitamin B metabolites, while illuminating how TCRs recognize microbial metabolic signatures.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major histocompatibility complex class I-related gene protein
A, C
271Homo sapiensGene Names: MR1
Find proteins for Q95460 (Homo sapiens)
Go to Gene View: MR1
Go to UniProtKB:  Q95460
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, F
99Homo sapiensGene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MAIT T-cell receptor alpha chain
D, G
203Homo sapiensGene Names: TRA@
Find proteins for Q6P4G7 (Homo sapiens)
Go to UniProtKB:  Q6P4G7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
MAIT T-cell receptor beta chain
E, H
245Homo sapiensGene Names: TRBC1
Find proteins for P01850 (Homo sapiens)
Go to UniProtKB:  P01850
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1VY
Query on 1VY

Download SDF File 
Download CCD File 
A, C
1-deoxy-1-(7-hydroxy-6-methyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol
C12 H16 N4 O7
COXMGTTXHPRZBO-BBVRLYRLSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1VYKd: 1650 nM BINDINGMOAD
1VYKd: 1650 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 218.370α = 90.00
b = 71.203β = 104.86
c = 144.642γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
Blu-Icedata collection
BUSTERrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-09-11
    Type: Database references