9QH0 | pdb_00009qh0

Escherichia coli polynucleotide phosphorylase in complex with recognition site of RNase E

• PDB DOI: https://doi.org/10.2210/pdb9QH0/pdb
• EM Map EMD-53151: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-03-14 Released: 2025-04-23 
• Deposition Author(s): Paris, G., Luisi, B.F.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.52 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Escherichia coli 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: electron microscopy

Macromolecule Content 

• Total Structure Weight: 185.12 kDa 
• Atom Count: 12,946 
• Modeled Residue Count: 1,702 
• Deposited Residue Count: 1,705 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyribonucleotide nucleotidyltransferase	A, B, C	549	Escherichia coli	Mutation(s): 0  Gene Names: pnp, b3164, JW5851 EC: 2.7.7.8
UniProt
Find proteins for P05055 (Escherichia coli (strain K12)) Explore P05055  Go to UniProtKB:  P05055

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease E	D	58	Escherichia coli	Mutation(s): 0  Gene Names: rne, ams, hmp1, b1084, JW1071 EC: 3.1.26.12
UniProt
Find proteins for P21513 (Escherichia coli (strain K12)) Explore P21513  Go to UniProtKB:  P21513

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.52 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-23 
Deposition Author(s): Paris, G., Luisi, B.F.

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

Revision History  

• Version 1.0: 2025-04-23
  Type: Initial release