9B2K | pdb_00009b2k

SpCas9 with dual-guide RNA in open conformation

PDB DOI: https://doi.org/10.2210/pdb9B2K/pdb
NAKB: 9B2K
EM Map EMD-44111: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Streptococcus pyogenes
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-15 Released: 2025-03-26
Deposition Author(s): Korolev, S., Gagnon, K.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.67 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9B2K

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

Literature

SpCas9 with dual-guide RNA and target DNA

Korolev, S., Gagnon, K.

To be published.

Macromolecule Content

Total Structure Weight: 196.72 kDa
Atom Count: 10,242
Modeled Residue Count: 1,136
Deposited Residue Count: 1,496
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas9/Csn1	C [auth P]	1,384	Streptococcus pyogenes	Mutation(s): 0 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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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 1
RNA (5'-R(PGPUPUPUPUPAPGPAPGPCPUPAPUPGPCPUPGPU)-3')	A	42	Streptococcus pyogenes
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 2
RNA (56-MER)	B	70	Streptococcus pyogenes
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.67 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.4.0
MODEL REFINEMENT	PHENIX	1.20.1

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-03-26
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.