9JHL | pdb_00009jhl

Cryo-EM structure of CpAgo_gDNA-tg_dsDNA dimeric ternary complex

• PDB DOI: https://doi.org/10.2210/pdb9JHL/pdb
• NAKB: 9JHL
• EM Map EMD-61486: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Clostridium perfringenosum, 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: 2.86 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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 203.5 kDa 
• Atom Count: 13,512 
• Modeled Residue Count: 1,560 
• Deposited Residue Count: 1,602 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Clostridium perfringen Argonaute	A, D [auth B]	751	Clostridium perfringenosum	Mutation(s): 0
UniProt
Find proteins for A0A343JEE2 (Clostridium isatidis) Explore A0A343JEE2  Go to UniProtKB:  A0A343JEE2

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], E [auth D]	21	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (29-MER)	C [auth E], F	29	synthetic construct

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.86 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