9KU3 | pdb_00009ku3

Cryo-EM structure of CtpA S300A/K325A/Q329A mutant from Helicobacter pylori

• PDB DOI: https://doi.org/10.2210/pdb9KU3/pdb
• NAKB: 9KU3
• EM Map EMD-62573: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Helicobacter pylori G27, Escherichia coli BL21(DE3)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-12-03 Released: 2025-12-03 
• Deposition Author(s): Sun, K., Zhang, H., Au, S.W.N.
• Funding Organization(s): The University Grants Committee, Research Grants Council (RGC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.14 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of CtpA S300A/K325A/Q329A mutant from Helicobacter pylori

Sun, K., Zhang, H., Au, S.W.N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B3C3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A3B3C1D1E1F1G1H1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 280.12 kDa 
• Atom Count: 17,769 
• Modeled Residue Count: 2,317 
• Deposited Residue Count: 2,544 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxyl-terminal protease	A, B, C, D, E, F	416	Helicobacter pylori G27	Mutation(s): 3  Gene Names: HPG27_1298
UniProt
Find proteins for B5Z8Z7 (Helicobacter pylori (strain G27)) Explore B5Z8Z7  Go to UniProtKB:  B5Z8Z7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Unidentified protein	G, H, I, J, K, L [auth M]	8	Escherichia coli BL21(DE3)	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.14 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: 2025-12-03 
Deposition Author(s): Sun, K., Zhang, H., Au, S.W.N.

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Funding Organization	Location	Grant Number
The University Grants Committee, Research Grants Council (RGC)	Hong Kong	14117622

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release
  
• Version 2.0: 2026-07-08
  Changes: Data collection, Derived calculations, Polymer sequence, Structure summary