9WAD | pdb_00009wad

Cryo-EM structure of AtCas9-sgRNA-B-form DNA ternary complex

• PDB DOI: https://doi.org/10.2210/pdb9WAD/pdb
• EM Map EMD-65812: EMDB EMDataResource

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


• Deposited: 2025-08-11 Released: 2026-07-01 
• Deposition Author(s): Meng, B., Duan, M., Wu, L.J., Liu, Z.J., Zhang, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.15 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation

Currently 9WAD does not have a validation slider image.

Literature

Structural basis of AtCas9 recognition of PAM mutants in underwound DNA topology

Duan, M., Meng, B., Zhou, L., Wu, L.J., Tong, X., Huang, D., Yin, H., Liu, Z.J., Zhang, Y.

(2026) Nat Struct Mol Biol 

• DOI: https://doi.org/10.1038/s41594-026-01831-6

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: 191.17 kDa 
• Atom Count: 8,590 
• Modeled Residue Count: 842 
• Deposited Residue Count: 1,341 
• 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	1,154	Alicyclobacillus tolerans	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
sgRNA	B	117	Alicyclobacillus tolerans

Entity ID: 3
Molecule	Chains	Length	Organism	Image
TS DNA	C	35	Alicyclobacillus tolerans

Entity ID: 4
Molecule	Chains	Length	Organism	Image
NTS DNA	D	35	Alicyclobacillus tolerans

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.15 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC	4.7

Structure Validation

Currently 9WAD does not have a validation slider image.

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-07-01 
Deposition Author(s): Meng, B., Duan, M., Wu, L.J., Liu, Z.J., Zhang, Y.

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

Revision History  

• Version 1.0: 2026-07-01
  Type: Initial release