8ZDA | pdb_00008zda

Cryo-EM structure of eSaCas9_NNG-guide RNA-target DNA complex in a catalytically active state

• PDB DOI: https://doi.org/10.2210/pdb8ZDA/pdb
• NAKB: 8ZDA
• EM Map EMD-39954: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-01 Released: 2025-11-05 
• Deposition Author(s): Omura, S.N., Nakagawa, R., Yamashita, K., Nishimasu, H., Nureki, O.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

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

Literature

Engineering a compact high-fidelity Staphylococcus aureus Cas9 variant with broader targeting range and mechanistic insights into its activation.

Omura, S.N., Nakagawa, R., Kajimoto, S., Okazaki, S., Ishiguro, S., Mori, H., Onishi, K., Kashiwakura, Y., Hiramoto, T., Hirano, H., Yamashita, K., Jividen, K., Tsai, S.Q., Yachie, N., Ohmori, T., Nishimasu, H., Nureki, O.

(2026) Nat Commun 

• DOI: https://doi.org/10.1038/s41467-026-71626-2

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: 182.93 kDa 
• Atom Count: 11,623 
• Modeled Residue Count: 1,149 
• Deposited Residue Count: 1,241 
• Unique protein chains: 1
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas9	A	1,056	Staphylococcus aureus	Mutation(s): 0  Gene Names: cas9 EC: 3.1
UniProt
Find proteins for J7RUA5 (Staphylococcus aureus) Explore J7RUA5  Go to UniProtKB:  J7RUA5

Entity ID: 2
Molecule	Chains	Length	Organism	Image
sgRNA	B	99	Staphylococcus aureus

Entity ID: 3
Molecule	Chains	Length	Organism	Image
Target DNA strand1	C	17	Staphylococcus aureus

Entity ID: 4
Molecule	Chains	Length	Organism	Image
Non-target DNA strand	D	43	Staphylococcus aureus

Entity ID: 5
Molecule	Chains	Length	Organism	Image
Target DNA strand2	E	26	Staphylococcus aureus

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	F [auth A], G [auth A], H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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	Servalcat	0.4.68

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Omura, S.N., Nakagawa, R., Yamashita, K., Nishimasu, H., Nureki, O.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	--
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release
  
• Version 1.1: 2026-04-15
  Changes: Data collection, Database references