5U6Q

Structure of human MR1-3-F-SA in complex with human MAIT A-F7 TCR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Drugs and drug-like molecules can modulate the function of mucosal-associated invariant T cells.

Keller, A.N.Eckle, S.B.Xu, W.Liu, L.Hughes, V.A.Mak, J.Y.Meehan, B.S.Pediongco, T.Birkinshaw, R.W.Chen, Z.Wang, H.D'Souza, C.Kjer-Nielsen, L.Gherardin, N.A.Godfrey, D.I.Kostenko, L.Corbett, A.J.Purcell, A.W.Fairlie, D.P.McCluskey, J.Rossjohn, J.

(2017) Nat. Immunol. 18: 402-411

  • DOI: 10.1038/ni.3679
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The major-histocompatibility-complex-(MHC)-class-I-related molecule MR1 can present activating and non-activating vitamin-B-based ligands to mucosal-associated invariant T cells (MAIT cells). Whether MR1 binds other ligands is unknown. Here we identi ...

    The major-histocompatibility-complex-(MHC)-class-I-related molecule MR1 can present activating and non-activating vitamin-B-based ligands to mucosal-associated invariant T cells (MAIT cells). Whether MR1 binds other ligands is unknown. Here we identified a range of small organic molecules, drugs, drug metabolites and drug-like molecules, including salicylates and diclofenac, as MR1-binding ligands. Some of these ligands inhibited MAIT cells ex vivo and in vivo, while others, including diclofenac metabolites, were agonists. Crystal structures of a T cell antigen receptor (TCR) from a MAIT cell in complex with MR1 bound to the non-stimulatory and stimulatory compounds showed distinct ligand orientations and contacts within MR1, which highlighted the versatility of the MR1 binding pocket. The findings demonstrated that MR1 was able to capture chemically diverse structures, spanning mono- and bicyclic compounds, that either inhibited or activated MAIT cells. This indicated that drugs and drug-like molecules can modulate MAIT cell function in mammals.


    Organizational Affiliation

    Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major histocompatibility complex class I-related gene protein
C, A
271Homo sapiensMutation(s): 0 
Gene Names: MR1
Find proteins for Q95460 (Homo sapiens)
Go to Gene View: MR1
Go to UniProtKB:  Q95460
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MAIT T-cell receptor alpha chain
D, B
203N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MAIT T-cell receptor beta chain
E, G
245N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
F, H
99Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
G
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
7ZS
Query on 7ZS

Download SDF File 
Download CCD File 
A, C
3-methanoyl-2-oxidanyl-benzoic acid
C8 H6 O4
YOEUNKPREOJHBW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 217.668α = 90.00
b = 70.510β = 104.77
c = 143.370γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research CouncilAustraliaCE140100011
National Health and Medical Research Council (Australia)AustraliaAF50

Revision History 

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence, Data collection
  • Version 1.2: 2017-11-22
    Type: Refinement description
  • Version 1.3: 2018-04-18
    Type: Data collection, Database references