4NQC

Crystal structure of TCR-MR1 ternary complex and covalently bound 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

T-cell activation by transitory neo-antigens derived from distinct microbial pathways.

Corbett, A.J.Eckle, S.B.Birkinshaw, R.W.Liu, L.Patel, O.Mahony, J.Chen, Z.Reantragoon, R.Meehan, B.Cao, H.Williamson, N.A.Strugnell, R.A.Van Sinderen, D.Mak, J.Y.Fairlie, D.P.Kjer-Nielsen, L.Rossjohn, J.McCluskey, J.

(2014) Nature 509: 361-365

  • DOI: https://doi.org/10.1038/nature13160
  • Primary Citation of Related Structures:  
    4NQC, 4NQD, 4NQE

  • PubMed Abstract: 

    T cells discriminate between foreign and host molecules by recognizing distinct microbial molecules, predominantly peptides and lipids. Riboflavin precursors found in many bacteria and yeast also selectively activate mucosal-associated invariant T (MAIT) cells, an abundant population of innate-like T cells in humans. However, the genesis of these small organic molecules and their mode of presentation to MAIT cells by the major histocompatibility complex (MHC)-related protein MR1 (ref. 8) are not well understood. Here we show that MAIT-cell activation requires key genes encoding enzymes that form 5-amino-6-d-ribitylaminouracil (5-A-RU), an early intermediate in bacterial riboflavin synthesis. Although 5-A-RU does not bind MR1 or activate MAIT cells directly, it does form potent MAIT-activating antigens via non-enzymatic reactions with small molecules, such as glyoxal and methylglyoxal, which are derived from other metabolic pathways. The MAIT antigens formed by the reactions between 5-A-RU and glyoxal/methylglyoxal were simple adducts, 5-(2-oxoethylideneamino)-6-D-ribitylaminouracil (5-OE-RU) and 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil (5-OP-RU), respectively, which bound to MR1 as shown by crystal structures of MAIT TCR ternary complexes. Although 5-OP-RU and 5-OE-RU are unstable intermediates, they became trapped by MR1 as reversible covalent Schiff base complexes. Mass spectra supported the capture by MR1 of 5-OP-RU and 5-OE-RU from bacterial cultures that activate MAIT cells, but not from non-activating bacteria, indicating that these MAIT antigens are present in a range of microbes. Thus, MR1 is able to capture, stabilize and present chemically unstable pyrimidine intermediates, which otherwise convert to lumazines, as potent antigens to MAIT cells. These pyrimidine adducts are microbial signatures for MAIT-cell immunosurveillance.


  • Organizational Affiliation

    1] Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia [2].


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major histocompatibility complex class I-related gene protein
A, C
271Homo sapiensMutation(s): 1 
Gene Names: MR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q95460 (Homo sapiens)
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Go to UniProtKB:  Q95460
PHAROS:  Q95460
GTEx:  ENSG00000153029 
Entity Groups  
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UniProt GroupQ95460
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, F
99Homo sapiensMutation(s): 0 
Gene Names: B2MBeta 2 microglobulinCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
TCR alpha chain
D, G
203Homo sapiensMutation(s): 0 
Gene Names: TCR-alpha
UniProt
Find proteins for Q6P4G7 (Homo sapiens)
Explore Q6P4G7 
Go to UniProtKB:  Q6P4G7
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UniProt GroupQ6P4G7
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
TCR beta chain
E, H
245Homo sapiensMutation(s): 0 
Gene Names: TCR-beta
UniProt
Find proteins for P01850 (Homo sapiens)
Explore P01850 
Go to UniProtKB:  P01850
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UniProt GroupP01850
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2LJ
Query on 2LJ

Download Ideal Coordinates CCD File 
I [auth A],
J [auth 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
NA
Query on NA

Download Ideal Coordinates CCD File 
K [auth H]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 218.76α = 90
b = 71.11β = 104.87
c = 144.28γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
BUSTERrefinement
MOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-05-28
    Changes: Database references
  • Version 1.2: 2014-11-19
    Changes: Structure summary