9KJ6 | pdb_00009kj6

Crystal Structure of SpCas9 ternary complex, amino acids (1242-1263) replaced with Gly-Ser linker

• PDB DOI: https://doi.org/10.2210/pdb9KJ6/pdb
• NAKB: 9KJ6

• Classification: DNA BINDING PROTEIN
• Organism(s): Streptococcus pyogenes, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-11-12 Released: 2025-11-12 
• Deposition Author(s): Kim, S., Bae, J., Choi, H.J.
• Funding Organization(s): Samsung Science and Technology Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.59 Å
• R-Value Free: 
  0.271 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of SpCas9 ternary complex, amino acids (1242-1263) replaced with Gly-Ser linker

Kim, S., Choi, H.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 211.17 kDa 
• Atom Count: 13,121 
• Modeled Residue Count: 1,479 
• Deposited Residue Count: 1,529 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas9/Csn1	A	1,357	Streptococcus pyogenes	Mutation(s): 2  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: 2
Molecule	Chains	Length	Organism	Image
single-guide RNA	B	102	Streptococcus pyogenes

Entity ID: 3
Molecule	Chains	Length	Organism	Image
Target Strand of double-stranded DNA	C	43	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
Non-target Strand of double-stranded DNA	D	27	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.59 Å
• R-Value Free:  0.271 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.55	α = 90
b = 146.85	β = 90
c = 222.36	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Kim, S., Bae, J., Choi, H.J.

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Funding Organization	Location	Grant Number
Samsung Science and Technology Foundation	Korea, Republic Of	SRFC-MA1801-09

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release