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

Literature

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

Paris, G., Luisi, B.F.

To be published.

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ZLT3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A602Z3X3
Sequence Annotations Expand
Reference Sequence

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-30

Deposition Author(s):

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

Revision History (Full details and data files)

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

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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.