9EK7 | pdb_00009ek7

Crystal structure of MAIT TCR in complex with MR1-5FdU


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.206 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Mitochondria regulate MR1 protein expression and produce self-metabolites that activate MR1-restricted T cells.

Prota, G.Berloffa, G.Awad, W.Vacchini, A.Chancellor, A.Schaefer, V.Constantin, D.Littler, D.R.Colombo, R.Nosi, V.Mori, L.Rossjohn, J.De Libero, G.

(2025) Proc Natl Acad Sci U S A 122: e2418525122-e2418525122

  • DOI: https://doi.org/10.1073/pnas.2418525122
  • Primary Citation Related Structures: 
    9EK6, 9EK7

  • PubMed Abstract: 

    Mitochondria coordinate several metabolic pathways, producing metabolites that influence the immune response in various ways. It remains unclear whether mitochondria impact antigen presentation by the MHC-class-I-related antigen-presenting molecule, MR1, which presents small molecules to MR1-restricted T-lymphocytes. Here, we demonstrate that mitochondrial complex III and the enzyme dihydroorotate dehydrogenase are essential for the cell-surface expression of MR1 and for generating uridine- and thymidine-related compounds that bind to MR1 and are produced upon oxidation by reactive oxygen species. One mitochondria-derived immunogenic formylated metabolite we identified is 5-formyl-deoxyuridine (5-FdU). Structural studies indicate that 5-FdU binds in the A'-antigen-binding pocket of MR1, positioning the deoxyribose toward the surface of MR1 for TCR interaction. 5-FdU stimulates specific T cells and detects circulating T cells when loaded onto MR1-tetramers. 5-FdU-reactive cells resemble adaptive T cells and express the phenotypes of naïve, memory, and effector cells, indicating prior in vivo stimulation. These findings suggest that mitochondria may play a role in MR1-mediated immune surveillance.


  • Organizational Affiliation
    • Experimental Immunology, Department of Biomedicine, University Hospital Basel, University of Basel, Basel 4031, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 189.62 kDa 
  • Atom Count: 13,963 
  • Modeled Residue Count: 1,608 
  • Deposited Residue Count: 1,642 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Major histocompatibility complex class I-related gene protein
A, C
271Homo sapiensMutation(s): 0 
Gene Names: MR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q95460 (Homo sapiens)
Explore Q95460 
Go to UniProtKB:  Q95460
PHAROS:  Q95460
GTEx:  ENSG00000153029 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ95460
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
TCR alpha
B, D
204Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
TCR beta
E, G
246Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
F, H
100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YC6
(Subject of Investigation/LOI)

Query on YC6



Download:Ideal Coordinates CCD File
I [auth A]1-(2-deoxy-alpha-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione
C10 H12 N2 O6
MVORBLZUGBSUNB-RNJXMRFFSA-N
THM
(Subject of Investigation/LOI)

Query on THM



Download:Ideal Coordinates CCD File
Q [auth C]THYMIDINE
C10 H14 N2 O5
IQFYYKKMVGJFEH-XLPZGREQSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
J [auth A]
M [auth A]
P [auth B]
R [auth C]
T [auth C]
J [auth A],
M [auth A],
P [auth B],
R [auth C],
T [auth C],
W [auth F],
X [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
K [auth A],
L [auth A],
O [auth B],
S [auth C],
U [auth E]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL



Download:Ideal Coordinates CCD File
N [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
V [auth E],
Y [auth G]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.206 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 217.587α = 90
b = 70.528β = 104.68
c = 144.227γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Database references