9T38 | pdb_00009t38

Rhs2-CT endonuclease toxin in complex with cognate immunity protein RhsI2 and EF-Tu

PDB DOI: https://doi.org/10.2210/pdb9T38/pdb

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Escherichia coli, Serratia marcescens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-10-27 Released: 2025-12-24
Deposition Author(s): Pankov, G., Hunter, W.N., Coulthurst, S.J.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.314 (Depositor), 0.316 (DCC)
R-Value Work:
0.270 (Depositor), 0.274 (DCC)

Starting Models: experimental, in silico
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

An Rhs effector uses distinct target cell functions to intoxicate bacterial and fungal competitors

Avelar, G.M., Pankov, G., Sarapa, T., Quinn, J., Hunter, W.N., Rickman, C., Coulthurst, S.J.

(2025) bioRxiv

DOI: https://doi.org/10.1101/2025.10.28.685041

Macromolecule Content

Total Structure Weight: 160.9 kDa
Atom Count: 10,491
Modeled Residue Count: 1,313
Deposited Residue Count: 1,436
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation factor Tu 2	A [auth C], D [auth F]	394	Escherichia coli	Mutation(s): 0 Gene Names: tufB, b3980, JW3943 EC: 3.6.5.3
UniProt
Find proteins for P0CE48 (Escherichia coli (strain K12)) Explore P0CE48 Go to UniProtKB: P0CE48
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CE48
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunity protein RhsI2	B, E	162	Serratia marcescens	Mutation(s): 0 Gene Names: FBF90_11815
UniProt
Find proteins for A0ABF7SXG6 (Serratia marcescens) Explore A0ABF7SXG6 Go to UniProtKB: A0ABF7SXG6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ABF7SXG6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhs-family protein	C [auth A], F [auth D]	162	Serratia marcescens	Mutation(s): 0 Gene Names: SMDB11_1610
UniProt
Find proteins for A0ABC9II69 (Serratia marcescens subsp. marcescens Db11) Explore A0ABC9II69 Go to UniProtKB: A0ABC9II69
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ABC9II69
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP (Subject of Investigation/LOI) Query on GDP Download:Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain K [auth F] MOL2 format, chain G [auth C] MOL2 format, chain K [auth F] mmCIF format, chain G [auth C] mmCIF format, chain K [auth F]	G [auth C], K [auth F]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain G [auth C] Focus chain K [auth F] Interactions & Density Focus chain G [auth C] Focus chain K [auth F]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain N [auth F] SDF format, chain J [auth C] MOL2 format, chain N [auth F] MOL2 format, chain J [auth C] mmCIF format, chain N [auth F] mmCIF format, chain J [auth C]	J [auth C], N [auth F]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain J [auth C] Focus chain N [auth F] Interactions & Density Focus chain J [auth C] Focus chain N [auth F]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth F] SDF format, chain H [auth C] MOL2 format, chain L [auth F] MOL2 format, chain H [auth C] mmCIF format, chain L [auth F] mmCIF format, chain H [auth C]	H [auth C], L [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Focus chain L [auth F] Interactions & Density Focus chain H [auth C] Focus chain L [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain M [auth F] SDF format, chain I [auth C] MOL2 format, chain M [auth F] MOL2 format, chain I [auth C] mmCIF format, chain M [auth F] mmCIF format, chain I [auth C]	I [auth C], M [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain M [auth F] Interactions & Density Focus chain I [auth C] Focus chain M [auth F]