43RH | pdb_000043rh

Crystal structure of TCR C3K in complex with H2-Q9/VP2.139

PDB DOI: https://doi.org/10.2210/pdb43RH/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Alphapolyomavirus muris
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-07-14 Released: 2026-07-29
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: 3.33 Å
R-Value Free:
0.267 (Depositor), 0.266 (DCC)
R-Value Work:
0.218 (Depositor), 0.218 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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: 144.54 kDa
Atom Count: 10,163
Modeled Residue Count: 1,266
Deposited Residue Count: 1,266
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histocompatibility 2, Q region locus 7	A	274	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

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	99	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01887
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor alpha variable 13D-1,T cell receptor alpha joining 18,T cell receptor alpha chain constant	C, F [auth E]	201	Mus musculus	Mutation(s): 0 Gene Names: Trav13d-1, Traj18, TRAC, TCRA
UniProt
Find proteins for A0A075B606 (Mus musculus) Explore A0A075B606 Go to UniProtKB: A0A075B606
Find proteins for A0A0G2JG46 (Mus musculus) Explore A0A0G2JG46 Go to UniProtKB: A0A0G2JG46
Find proteins for P01848 (Homo sapiens) Explore P01848 Go to UniProtKB: P01848
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	A0A075B606 P01848 A0A0G2JG46
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor beta, variable 2,T cell receptor beta joining 1-1,T cell receptor beta constant 1	D, G [auth F]	241	Mus musculus	Mutation(s): 0 Gene Names: Trbv2, Trbj1-1, TRBC1
UniProt
Find proteins for A0A0B4J1G8 (Mus musculus) Explore A0A0B4J1G8 Go to UniProtKB: A0A0B4J1G8
Find proteins for A0A0A6YVY0 (Mus musculus) Explore A0A0A6YVY0 Go to UniProtKB: A0A0A6YVY0
Find proteins for P01850 (Homo sapiens) Explore P01850 Go to UniProtKB: P01850
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	A0A0A6YVY0 A0A0B4J1G8 P01850
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Minor capsid protein VP2	E [auth P]	9	Alphapolyomavirus muris	Mutation(s): 0
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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain J [auth B]	H [auth A] J [auth B] K [auth B] L [auth B] N [auth C] H [auth A], J [auth B], K [auth B], L [auth B], N [auth C], O [auth C], P [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth B] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B]	I [auth A], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Interactions & Density Focus chain I [auth A] Focus chain M [auth B]