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

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
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This is version 1.0 of the entry. See complete history.

Literature

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

Kim, S., Choi, H.J.

To be published.

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99ZW2
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 2
single-guide RNA	B	102	Streptococcus pyogenes
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Reference Sequence

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

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

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-12

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.