9IBH | pdb_00009ibh

Salmonella typhimurium polynucleotide phosphorylase in complex with recognition site of RNase E

• PDB DOI: https://doi.org/10.2210/pdb9IBH/pdb
• EM Map EMD-52810: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-02-12 Released: 2025-07-30 
• Deposition Author(s): Paris, G., Luisi, B.F.
• Funding Organization(s): Wellcome Trust

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Salmonella typhimurium polynucleotide phosphorylase in complex with recognition site of RNase E

Paris, G., Luisi, B.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 183.93 kDa 
• Atom Count: 12,906 
• Modeled Residue Count: 1,691 
• Deposited Residue Count: 1,696 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyribonucleotide nucleotidyltransferase	A, B, C	546	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: pnp, STM3282 EC: 2.7.7.8
UniProt
Find proteins for Q8ZLT3 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZLT3  Go to UniProtKB:  Q8ZLT3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease E	D	58	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: rne, CAI81_13325 EC: 3.1.26.12
UniProt
Find proteins for A0A602Z3X3 (Salmonella enterica subsp. enterica serovar Pensacola) Explore A0A602Z3X3  Go to UniProtKB:  A0A602Z3X3

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Paris, G., Luisi, B.F.

---

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	222451/Z/21/Z

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release