9JL1 | pdb_00009jl1

SpCas9 with mini-gRNA conformation

PDB DOI: https://doi.org/10.2210/pdb9JL1/pdb
EM Map EMD-61575: EMDB EMDataResource
NAKB: 9JL1

Classification: RNA BINDING PROTEIN
Organism(s): Streptococcus pyogenes serotype M1, unclassified sequences
Expression System: Escherichia coli BL21(DE3), unclassified sequences
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: 3.50 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

SpCas9 with mini-gRNA conformation

Xi, Z.

To be published.

Macromolecule Content

Total Structure Weight: 190.34 kDa
Atom Count: 9,003
Modeled Residue Count: 1,056
Deposited Residue Count: 1,466
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas9/Csn1	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

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
gRNA	B	98	unclassified sequences
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

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.