9JH7 | pdb_00009jh7

Cryo-EM structure of CpAgo in complex with the 5'-P guide DNA.

• PDB DOI: https://doi.org/10.2210/pdb9JH7/pdb
• EM Map EMD-61474: EMDB EMDataResource
• NAKB: 9JH7

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Clostridium perfringens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-09 Released: 2025-07-30 
• Deposition Author(s): Liu, Y., Li, S., Zhang, K.
• Funding Organization(s): Other government

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Dimeric state and novel nucleotide-binding pocket drive CpAgo-mediated DNA cleavage

Liu, Y., Li, S., Zhang, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 92.92 kDa 
• Atom Count: 6,357 
• Modeled Residue Count: 760 
• Deposited Residue Count: 772 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Clostridium perfringens Argonaute (CpAgo)	A	751	Clostridium perfringens	Mutation(s): 0
UniProt
Find proteins for A0AAW4IU58 (Clostridium perfringens) Explore A0AAW4IU58  Go to UniProtKB:  A0AAW4IU58

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3')	B [auth C]	21	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	4.5.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Liu, Y., Li, S., Zhang, K.

---

Funding Organization	Location	Grant Number
Other government		--

Revision History  

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