5U1R

Structure of human MR1-diclofenac in complex with human MAIT A-F7 TCR

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

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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:  
    5U16, 5U17, 5U1R, 5U2V, 5U6Q

  • 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 identified a range of small organic molecules, drugs, drug metabolites and drug-like molecules, including salicylates and diclofenac, as MR1-binding ligands ...

    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: 

    Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major histocompatibility complex class I-related gene proteinE [auth A],
A [auth C]		271Homo sapiensMutation(s): 0 
Gene Names: MR1
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Find proteins for Q95460 (Homo sapiens)
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PHAROS:  Q95460
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UniProt GroupQ95460
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MAIT T-cell receptor alpha chainF [auth B],
B [auth D]		203Homo sapiensMutation(s): 0 
Gene Names: B2M
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MAIT T-cell receptor beta chainC [auth E],
G		245Homo sapiensMutation(s): 0 
Gene Names: TRAV/TRAC
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinD [auth F],
H		100Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
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Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
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UniProt GroupP61769
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.571α = 90
b = 69.65β = 103.38
c = 142.85γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaCE140100011
Australian Research Council (ARC)AustraliaAF50

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Database references, Derived calculations
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence, Data collection