8BP6 | pdb_00008bp6

Structure of MHC-class I related molecule MR1 with bound M3Ade.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.247 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 
    0.236 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The carbonyl nucleobase adduct M 3 Ade is a potent antigen for adaptive polyclonal MR1-restricted T cells.

Chancellor, A.Constantin, D.Berloffa, G.Yang, Q.Nosi, V.Loureiro, J.P.Colombo, R.Jakob, R.P.Joss, D.Pfeffer, M.De Simone, G.Morabito, A.Schaefer, V.Vacchini, A.Brunelli, L.Montagna, D.Heim, M.Zippelius, A.Davoli, E.Haussinger, D.Maier, T.Mori, L.De Libero, G.

(2024) Immunity 

  • DOI: https://doi.org/10.1016/j.immuni.2024.11.019
  • Primary Citation of Related Structures:  
    8BP6

  • PubMed Abstract: 

    The major histocompatibility complex (MHC) class I-related molecule MHC-class-I-related protein 1 (MR1) presents metabolites to distinct MR1-restricted T cell subsets, including mucosal-associated invariant T (MAIT) and MR1T cells. However, self-reactive MR1T cells and the nature of recognized antigens remain underexplored. Here, we report a cell endogenous carbonyl adduct of adenine (8-(9H-purin-6-yl)-2-oxa-8-azabicyclo[3.3.1]nona-3,6-diene-4,6-dicarbaldehyde [M 3 Ade]) sequestered in the A' pocket of MR1. M 3 Ade induced in vitro MR1-mediated stimulation of MR1T cell clones that bound MR1-M 3 Ade tetramers. MR1-M 3 Ade tetramers identified heterogeneous MR1-reactive T cells ex vivo in healthy donors, individuals with acute myeloid leukemia, and tumor-infiltrating lymphocytes from non-small cell lung adenocarcinoma and hepatocarcinoma. These cells displayed phenotypic, transcriptional, and functional diversity at distinct differentiation stages, indicating their adaptive nature. They were also polyclonal, with some preferential T cell receptor (TCRαβ) pair usage. Thus, M 3 Ade is an MR1-presented self-metabolite that enables stimulation and tracking of human-MR1T cells from blood and tissue, aiding our understanding of their roles in health and disease.


  • Organizational Affiliation
    • Experimental Immunology, Department of Biomedicine, University Hospital Basel, University of Basel, 4031 Basel, Switzerland. Electronic address: andrew.chancellor@unibas.ch.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin,Major histocompatibility complex class I-related gene protein
A, B
384Homo sapiensMutation(s): 0 
Gene Names: B2MMR1
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
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 GroupsQ95460P61769
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.247 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.352α = 90
b = 143.534β = 101.82
c = 77.029γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-29
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Structure summary
  • Version 1.2: 2025-01-08
    Changes: Database references
  • Version 1.3: 2025-02-05
    Changes: Database references, Structure summary