9KO9 | pdb_00009ko9

Cryo-EM structure of PsCas9-sgRNA binary complex

PDB DOI: https://doi.org/10.2210/pdb9KO9/pdb
NAKB: 9KO9
EM Map EMD-62471: EMDB EMDataResource

Classification: RNA BINDING PROTEIN/RNA
Organism(s): Parasutterella secunda
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-11-20 Released: 2025-07-30
Deposition Author(s): Shen, P.P., Lu, X.Y., Huang, J.-W., Chen, C.-C., Gut, R.-T.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9KO9

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

Literature

Structural and Mechanistic Investigations of a High-Fidelity Cas9 from Parasutterella secunda

Shen, P., Lu, X., Wang, C., Huang, J.W., Min, J., Luo, J., Sun, Y., Chen, C.C., Guo, R.T.

(2025) ACS Catal 15: 10109-10118

DOI: https://doi.org/10.1021/acscatal.5c02993

Macromolecule Content

Total Structure Weight: 207.32 kDa
Atom Count: 13,851
Modeled Residue Count: 1,523
Deposited Residue Count: 1,566
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas9	A	1,435	Parasutterella secunda	Mutation(s): 0
UniProt
Find proteins for A0ABF7PQ28 (Parasutterella secunda) Explore A0ABF7PQ28 Go to UniProtKB: A0ABF7PQ28
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ABF7PQ28
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 2
RNA (131-MER)	B	131	Parasutterella secunda
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-30

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-07-30
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.