8BP6

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 
• R-Value Work: 0.237 
• R-Value Observed: 0.236 

Literature

The carbonyl nucleoside adduct M3Ade stabilizes MR1 and activates MR1-restricted self- and tumor-reactive T cells

Chancellor, A., Berloffa, G., Jakob, R.P., Maier, T., de Libero, G.

To be published.

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 
• Modelled 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 Q95460 (Homo sapiens) Explore Q95460  Go to UniProtKB:  Q95460
PHAROS:  Q95460 GTEx:  ENSG00000153029
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710
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 
• R-Value Work: 0.237 
• R-Value Observed: 0.236 
• 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