9WDX | pdb_00009wdx

Structure of SpCas9 with engineered disulfide bonds (R1210C/V1280C and L1119C/P1128C)

PDB DOI: https://doi.org/10.2210/pdb9WDX/pdb
EM Map EMD-65909: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Streptococcus pyogenes serotype M1
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2025-08-19 Released: 2026-08-26
Deposition Author(s): Teo, Z.T., Ravi, L.R.V., Jia, X., Xue, B., Qu, K., Yew, W.S.
Funding Organization(s): Other private, Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.72 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9WDX

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

Literature

Engineering Enhanced Thermostability and High-Temperature Activity in SpCas9 through Strategic C-Terminal Domain Disulfide Bond Incorporation

Teo, Z.T., Hartono, Y.D., Xue, B., Jia, X., Ravi, L.R.V., Qu, K., Carstens, C.-P., Bruhn, L., Yew, W.S.

To be published.

Macromolecule Content

Total Structure Weight: 159.92 kDa
Atom Count: 8,373
Modeled Residue Count: 1,030
Deposited Residue Count: 1,379
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas9/Csn1	A [auth P]	1,379	Streptococcus pyogenes serotype M1	Mutation(s): 4 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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.72 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286
RECONSTRUCTION	cryoSPARC	4.5.3

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	Singapore	I1901E0040
Other private	Singapore	I2301E0021
Other government	Singapore	NUHSRO/2022/033/Startup/03

Revision History (Full details and data files)

Version 1.0: 2026-08-26
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.