9JL2 | pdb_00009jl2

Classical conformation for the spCas9 with gRNA and target DNA complex

PDB DOI: https://doi.org/10.2210/pdb9JL2/pdb
NAKB: 9JL2
EM Map EMD-61576: EMDB EMDataResource

Classification: RNA BINDING PROTEIN
Organism(s): unclassified sequences, Streptococcus pyogenes serotype M1
Expression System: unclassified sequences, Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-09-17 Released: 2025-09-24
Deposition Author(s): Xi, Z.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Classical conformation for the spCas9 with gRNA and target DNA complex

Xi, Z.

To be published.

Macromolecule Content

Total Structure Weight: 207.55 kDa
Atom Count: 12,003
Modeled Residue Count: 1,259
Deposited Residue Count: 1,522
Unique protein chains: 1
Unique nucleic acid chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas9/Csn1	C [auth A]	1,368	Streptococcus pyogenes serotype M1	Mutation(s): 0 Gene Names: cas9 EC: 3.1
UniProt
Find proteins for Q99ZW2 (Streptococcus pyogenes serotype M1) Explore Q99ZW2 Go to UniProtKB: Q99ZW2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99ZW2
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
TS	A [auth C]	28	unclassified sequences
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
NTS	B [auth D]	28	unclassified sequences
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Length	Organism	Image
gRNA	D [auth B]	98	unclassified sequences
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History (Full details and data files)

Version 1.0: 2025-09-24
Type: Initial release

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.