8BP6 | pdb_00008bp6

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

• PDB DOI: https://doi.org/10.2210/pdb8BP6/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-11-16 Released: 2023-11-29 
• Deposition Author(s): Berloffa, G., Jakob, R.P., Maier, T.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.247 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

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 

• PubMed: 39701104 
• DOI: https://doi.org/10.1016/j.immuni.2024.11.019
• Primary Citation 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.

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Organizational Affiliation: 
• Experimental Immunology, Department of Biomedicine, University Hospital Basel, University of Basel, 4031 Basel, Switzerland. Electronic address: [e-mail].
Experimental Immunology, Department of Biomedicine, University Hospital Basel, University of Basel, 4031 Basel, Switzerland.
Experimental Immunology, Department of Biomedicine, University Hospital Basel, University of Basel, 4031 Basel, Switzerland; Department of Molecular Biotechnology and Health Sciences, University of Torino, 10126 Torino, Italy.
Biozentrum, University of Basel, 4056 Basel, Switzerland.
Department of Chemistry, University of Basel, 4056 Basel, Switzerland.
Department of Environmental Health Science, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milano, Italy.
Department of Sciences Clinic-Surgical, Diagnostic and Pediatric, University of Pavia and Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy.
Hepatology Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4031 Basel, Switzerland.
Cancer Immunology, Department of Biomedicine, University of Basel and University Hospital Basel, 4031 Basel, Switzerland.
Experimental Immunology, Department of Biomedicine, University Hospital Basel, University of Basel, 4031 Basel, Switzerland. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 89.2 kDa 
• Atom Count: 6,156 
• Modeled Residue Count: 737 
• Deposited Residue Count: 768 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin,Major histocompatibility complex class I-related gene protein	A, B	384	Homo sapiens	Mutation(s): 0  Gene Names: B2M, MR1
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
UniProt Groups	Q95460P61769

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R8F (Subject of Investigation/LOI)	C [auth A], D [auth B]	(1R,5S)-8-(9H-purin-6-yl)-2-oxa-8-azabicyclo[3.3.1]nona-3,6-diene-4,6-dicarbaldehyde C14 H11 N5 O3 JDSDLPGCRCFXJZ-WDEREUQCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.247 (Depositor), 0.240 (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 = 50.352	α = 90
b = 143.534	β = 101.82
c = 77.029	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): Berloffa, G., Jakob, R.P., Maier, T.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History  

• 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
• Version 1.4: 2026-03-04
  Changes: Refinement description