9JHM | pdb_00009jhm

Cryo-EM structure of CpAgo_gDNA-tg_bubble_dsDNA monomeric ternary complex

• PDB DOI: https://doi.org/10.2210/pdb9JHM/pdb
• EM Map EMD-61487: EMDB EMDataResource
• NAKB: 9JHM

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


• Deposited: 2024-09-10 Released: 2025-07-30 
• Deposition Author(s): Liu, Y., Li, S., Zhang, K.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 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: 110.65 kDa 
• Atom Count: 6,755 
• Modeled Residue Count: 780 
• Deposited Residue Count: 830 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Clostridium perfringen Argonaute	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

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (58-MER)	C [auth E]	58	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN (Subject of Investigation/LOI)	D [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 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.

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Funding Organization	Location	Grant Number
Other government		--

Revision History  

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