6PUF

Structure of human MAIT A-F7 TCR in complex with human MR1-5'D-5-OP-RU


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The molecular basis underpinning the potency and specificity of MAIT cell antigens.

Awad, W.Ler, G.J.M.Xu, W.Keller, A.N.Mak, J.Y.W.Lim, X.Y.Liu, L.Eckle, S.B.G.Le Nours, J.McCluskey, J.Corbett, A.J.Fairlie, D.P.Rossjohn, J.

(2020) Nat Immunol 21: 400-411

  • DOI: 10.1038/s41590-020-0616-6
  • Primary Citation of Related Structures:  
    6PUL, 6PUK, 6PUM, 6PUD, 6PUC, 6PUF, 6PUE, 6PUH, 6PUG, 6PUJ

  • PubMed Abstract: 
  • Mucosal-associated invariant T (MAIT) cells are activated by microbial riboflavin-based metabolite antigens when presented by MR1. How modifications to the potent antigen 5-OP-RU affect presentation by MR1 and MAIT cell activation remains unclear. He ...

    Mucosal-associated invariant T (MAIT) cells are activated by microbial riboflavin-based metabolite antigens when presented by MR1. How modifications to the potent antigen 5-OP-RU affect presentation by MR1 and MAIT cell activation remains unclear. Here we design 20 derivatives, termed altered metabolite ligands (AMLs), to dissect the impact of different antigen components on the human MAIT-MR1 axis. Analysis of 11 crystal structures of MAIT T cell antigen receptor (TCR)-MR1-AML ternary complexes, along with biochemical and functional assays, shows that MR1 cell-surface upregulation is influenced by ribityl and non-ribityl components of the ligand and the hydrophobicity of the MR1-AML interface. The polar ribityl chain of the AML strongly influences MAIT cell activation potency through dynamic compensatory interactions within a MAIT TCR-MR1-AML interaction triad. We define the basis by which the MAIT TCR can differentially recognize AMLs, thereby providing insight into MAIT cell antigen specificity and potency.


    Organizational Affiliation

    Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK. jamie.rossjohn@monash.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major histocompatibility complex class I-related gene proteinAC271Homo sapiensMutation(s): 0 
Gene Names: MR1
Find proteins for Q95460 (Homo sapiens)
Explore Q95460 
Go to UniProtKB:  Q95460
NIH Common Fund Data Resources
PHAROS  Q95460
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinBF100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Human TCR alpha chainDG204Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Human TCR beta chainEH246Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2LJ
Query on 2LJ

Download CCD File 
A, C
1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol
C12 H20 N4 O6
YCMPUNANLDFPQG-FHZGFTDOSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, C, F, H
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
F, H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 216.033α = 90
b = 69.815β = 104.26
c = 142.942γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASESphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-07-18 
  • Released Date: 2020-02-19 
  • Deposition Author(s): Awad, W., Rossjohn, J.

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

Revision History 

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-03-11
    Changes: Database references
  • Version 1.2: 2020-03-18
    Changes: Database references
  • Version 1.3: 2020-04-01
    Changes: Database references