9KOR | pdb_00009kor

Cryo-EM structure of PsCas9-sgRNA-dsDNA ternary complex

• PDB DOI: https://doi.org/10.2210/pdb9KOR/pdb
• EM Map EMD-62479: EMDB EMDataResource
• NAKB: 9KOR

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


• Deposited: 2024-11-21 Released: 2025-07-30 
• Deposition Author(s): Shen, P.P., Lu, X.Y., Huang, J.-W., Chen, C.-C., Guo, R.-T.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural and Mechanistic Investigations of a High-Fidelity Cas9 from Parasutterella secunda

Shen, P., Lu, X., Wang, C., Huang, J.W., Min, J., Luo, J., Sun, Y., Chen, C.C., Guo, R.T.

(2025) ACS Catal 15: 10109-10118

• DOI: https://doi.org/10.1021/acscatal.5c02993

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 222.74 kDa 
• Atom Count: 13,176 
• Modeled Residue Count: 1,379 
• Deposited Residue Count: 1,616 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas9	A	1,435	Parasutterella secunda	Mutation(s): 0
UniProt
Find proteins for A0ABF7PQ28 (Parasutterella secunda) Explore A0ABF7PQ28  Go to UniProtKB:  A0ABF7PQ28

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (131-MER)	B	131	Parasutterella secunda

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (25-mer)	C	25	Parasutterella secunda

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (25-MER)	D	25	Parasutterella secunda

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth B], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Shen, P.P., Lu, X.Y., Huang, J.-W., Chen, C.-C., Guo, R.-T.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

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