9CGS image
Entry Detail
PDB ID:
9CGS
Keywords:
Title:
Structure of human MAIT A-F7 TCR in complex with human MR1-Pyridoxal-5'-phosphate
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2024-06-30
Release Date:
2024-11-27
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.20
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Major histocompatibility complex class I-related gene protein
Chain IDs:A, C
Chain Length:271
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Beta-2-microglobulin
Chain IDs:B, F
Chain Length:100
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:TCR TRAV1-2
Chain IDs:D, G
Chain Length:204
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:TCR TRBV6-1
Chain IDs:E, H
Chain Length:246
Number of Molecules:2
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
LLP A LYS modified residue
Primary Citation
MR1 presents vitamin B6-related compounds for recognition by MR1-reactive T cells.
Proc.Natl.Acad.Sci.USA 121 e2414792121 e2414792121 (2024)
PMID: 39589872 DOI: 10.1073/pnas.2414792121

Abstact

The major histocompatibility complex class I related protein (MR1) presents microbially derived vitamin B2 precursors to mucosal-associated invariant T (MAIT) cells. MR1 can also present other metabolites to activate MR1-restricted T cells expressing more diverse T cell receptors (TCRs), some with anti-tumor reactivity. However, knowledge of the range of the antigen(s) that can activate diverse MR1-reactive T cells remains incomplete. Here, we identify pyridoxal (vitamin B6) as a naturally presented MR1 ligand using unbiased mass spectrometry analyses of MR1-bound metabolites. Pyridoxal, and the related compound, pyridoxal 5-phosphate bound to MR1 and enabled cell surface upregulation of wild type MR1*01 and MR1 expressing the Arg9His polymorphism associated with the MR1*04 allotype in a manner dependent on Lys43-mediated Schiff-base formation. Crystal structures of MR1*01 in complex with pyridoxal and pyridoxal 5-phosphate showed how these ligands were accommodated within the A-pocket of MR1. T cell lines transduced with the 7.G5 TCR, which has reported "pan-cancer" specificity, were specifically activated by pyridoxal presented by antigen-presenting cells expressing MR1*01 and MR1 allotypes bearing the less common Arg9His polymorphism. 7.G5 T cells also recognized, to a lesser extent, pyridoxal 5-phosphate and, importantly, recognition of both vitamers was blocked by an anti-MR1 antibody. 7.G5 TCR reactivity toward pyridoxal was enhanced when presented by the Arg9His polymorphism-bearing MR1 allotypes. Vitamin B6, and vitamers thereof, have been associated with various cancers, and here we describe a link between this ligand, MR1, and its allomorphs, and the pan-cancer 7.G5 TCR. This work identifies an MR1 ligand that can activate a diverse MR1-restricted TCR.

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Primary Citation of related structures