43SK | pdb_000043sk

Crystal structure of H2-Q9/VP2.139 peptide H1A mutant

PDB DOI: https://doi.org/10.2210/pdb43SK/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Alphapolyomavirus muris
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2026-07-15 Released: 2026-07-22
Deposition Author(s): Tennant, L., Jobichen, C., Tran, M.T., Littler, D.R., Farenc, C., Gras, S., Lukacher, A.E., Sullivan, L.C., Brooks, A.G., Rossjohn, J.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.246 (Depositor), 0.249 (DCC)
R-Value Work:
0.209 (Depositor), 0.211 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 43SK

This is version 1.0 of the entry. See complete history.

Literature

A murine MHC-Ib molecule, H2-Q9, drives peptide-centric T cell receptor recognition of a viral antigen

Tennant, L., Jobichen, C., Tran, M.T., Littler, D.R., Farenc, C., Gras, S., Lukacher, A.E., Sullivan, L.C., Brooks, A.G., Rossjohn, J.

To be published.

Macromolecule Content

Total Structure Weight: 44.83 kDa
Atom Count: 3,266
Modeled Residue Count: 384
Deposited Residue Count: 386
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histocompatibility 2, Q region locus 7	A	277	Mus musculus	Mutation(s): 0 Gene Names: H2-Q9, H2-Q7
UniProt
Find proteins for Q52PG7 (Mus musculus) Explore Q52PG7 Go to UniProtKB: Q52PG7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q52PG7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	Mus musculus	Mutation(s): 1 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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01887
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Minor capsid protein VP2	C [auth P]	9	Alphapolyomavirus muris	Mutation(s): 1
UniProt
Find proteins for P03097 (Murine polyomavirus (strain A3)) Explore P03097 Go to UniProtKB: P03097
Entity Groups
UniProt Group	P03097
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.246 (Depositor), 0.249 (DCC)
R-Value Work: 0.209 (Depositor), 0.211 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.619	α = 90
b = 56.799	β = 90
c = 119.314	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	--

Revision History (Full details and data files)

Version 1.0: 2026-07-22
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.