9AR6 | pdb_00009ar6

CryoEM structure of ThermoCas9 in pre-cleavage state bound with the DNA containing NNNNCCA PAM

• PDB DOI: https://doi.org/10.2210/pdb9AR6/pdb
• NAKB: 9AR6
• EM Map EMD-43771: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN/DNA/RNA
• Organism(s): Geobacillus thermodenitrificans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-02-22 Released: 2025-02-26 
• Deposition Author(s): Zhao, Y., Shu, Y., Li, H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.77 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Molecular basis for methylation-sensitive editing by Cas9

Roth, M.O., Shu, Y., Zhao, Y., Trasanidou, D., Hoffman, R.D., Trasanidis, N., Gelasco, M.K., Medina, M.L., Das, D., Rai, J., Wang, B., Li, H.

(2026) Nature 

• DOI: https://doi.org/10.1038/s41586-026-10384-z

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 189.63 kDa 
• Atom Count: 12,185 
• Modeled Residue Count: 1,226 
• Deposited Residue Count: 1,281 
• 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	1,082	Geobacillus thermodenitrificans	Mutation(s): 0  Gene Names: cas9-2, cas9, GTHT12_03401 EC: 3.1

Entity ID: 2
Molecule	Chains	Length	Organism	Image
non-target DNA	B [auth D]	12	Geobacillus thermodenitrificans

Entity ID: 3
Molecule	Chains	Length	Organism	Image
target-strand DNA	C [auth P]	40	Geobacillus thermodenitrificans

Entity ID: 4
Molecule	Chains	Length	Organism	Image
single guide RNA	D [auth B]	147	Geobacillus thermodenitrificans

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA (Subject of Investigation/LOI)	E [auth B], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.77 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-26 
Deposition Author(s): Zhao, Y., Shu, Y., Li, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM099604

Revision History  

• Version 1.0: 2025-02-26
  Type: Initial release
  
• Version 1.1: 2026-04-15
  Changes: Data collection, Database references