9B2K | pdb_00009b2k

SpCas9 with dual-guide RNA in open conformation

• PDB DOI: https://doi.org/10.2210/pdb9B2K/pdb
• NAKB: 9B2K
• EM Map EMD-44111: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Streptococcus pyogenes
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-15 Released: 2025-03-26 
• Deposition Author(s): Korolev, S., Gagnon, K.
• 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: 3.67 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

SpCas9 with dual-guide RNA and target DNA

Korolev, S., Gagnon, K.

To be published.

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: 196.72 kDa 
• Atom Count: 10,242 
• Modeled Residue Count: 1,136 
• Deposited Residue Count: 1,496 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas9/Csn1	C [auth P]	1,384	Streptococcus pyogenes	Mutation(s): 0  Gene Names: cas9, csn1, SPy_1046 EC: 3.1
UniProt
Find proteins for Q99ZW2 (Streptococcus pyogenes serotype M1) Explore Q99ZW2  Go to UniProtKB:  Q99ZW2

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*UP*UP*UP*UP*AP*GP*AP*GP*CP*UP*AP*UP*GP*CP*UP*GP*U)-3')	A	42	Streptococcus pyogenes

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (56-MER)	B	70	Streptococcus pyogenes

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.67 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.4.0
MODEL REFINEMENT	PHENIX	1.20.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-26 
Deposition Author(s): Korolev, S., Gagnon, K.

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

Revision History  

• Version 1.0: 2025-03-26
  Type: Initial release