8P43

Structure of the MHC class Ib molecule Qa-1b in complex with Q001 peptide

• PDB DOI: https://doi.org/10.2210/pdb8P43/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-05-19 Released: 2024-06-12 
• Deposition Author(s): Sala, B.M., Achour, A.
• Funding Organization(s): Cancerfonden, Swedish Research Council, Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.247 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 

Literature

MHC-E is a convergent checkpoint ligand for LILRB1 on macrophages and during inflammation for NKG2A on lymphocytes

Middelburg, J., Ghaffari, S., Schoufour, T., Sluijter, M., Schaap, G., Goynuk, B., Sala, B.M., Al-Tamimi, L., Scheeren, F., Franken, K.L.M.C., Joosten, S., Derksen, I., Neefjes, J., van der Burg, S., Achour, A., Wijdeven, R.H.M., Weidanz, J., van Hall, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 45.55 kDa 
• Atom Count: 3,307 
• Modelled Residue Count: 386 
• Deposited Residue Count: 386 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, Qa-1b	A	277	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	Mus musculus	Mutation(s): 0  Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus) Explore P01887  Go to UniProtKB:  P01887
IMPC:  MGI:88127

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Q001 peptide	C [auth P]	9	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.247 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.56	α = 90
b = 72.797	β = 90
c = 96.515	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
AutoProcess	data reduction
TRUNCATE	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-12 
Deposition Author(s): Sala, B.M., Achour, A.

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Funding Organization	Location	Grant Number
Cancerfonden	Sweden	grant 21 1605 Pj01H
Swedish Research Council	Sweden	grant 2021 05061
Other government		grant 10399

Revision History  

• Version 1.0: 2024-06-12
  Type: Initial release