9AR5 | pdb_00009ar5

Structure of Acidothermus cellulolyticus Cas9 bound with methylated DNA

• PDB DOI: https://doi.org/10.2210/pdb9AR5/pdb
• EM Map EMD-43770: EMDB EMDataResource
• NAKB: 9AR5

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


• Deposited: 2024-02-22 Released: 2025-02-26 
• Deposition Author(s): Das, A., Rai, J., Wang, B., 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: 2.88 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Molecular Basis for Epigenetic-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.

To be published.

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: 172.77 kDa 
• Atom Count: 11,414 
• Modeled Residue Count: 1,233 
• Deposited Residue Count: 1,280 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease, Csn1 family	A	1,138	Acidothermus cellulolyticus	Mutation(s): 0  Gene Names: Acel_1951
UniProt
Find proteins for A0LWB3 (Acidothermus cellulolyticus (strain ATCC 43068 / DSM 8971 / 11B)) Explore A0LWB3  Go to UniProtKB:  A0LWB3

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (92-MER)	B	106	Acidothermus cellulolyticus

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (25-MER)	C [auth X]	25	Acidothermus cellulolyticus

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-D(P*TP*AP*CP*A)-R(P*(5MC))-D(P*CP*AP*AP*GP*CP*T)-3')	D	11	Acidothermus cellulolyticus

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.88 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): Das, A., Rai, J., Wang, B., 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