9K4H | pdb_00009k4h

SuperFi Cas9 - mismatch 22nt sgRNA - DNA ternary complex class3

PDB DOI: https://doi.org/10.2210/pdb9K4H/pdb
NAKB: 9K4H
EM Map EMD-62059: EMDB EMDataResource

Classification: IMMUNE SYSTEM/DNA/RNA
Organism(s): Streptococcus pyogenes, synthetic construct
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-10-21 Released: 2025-10-22
Deposition Author(s): Zheng, R., Ma, L.J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.36 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

5' extended gRNA increases the cleavage activity of SuperFi-Cas9

Zheng, R., Ma, L.J.

To be published.

Macromolecule Content

Total Structure Weight: 222.09 kDa
Atom Count: 12,038
Modeled Residue Count: 1,262
Deposited Residue Count: 1,570
Unique protein chains: 1
Unique nucleic acid chains: 3

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	Mutation(s): 7 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99ZW2
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (50-MER)	B	50	synthetic construct
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (50-MER)	C	50	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA (102-MER)	D	102	synthetic construct
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.36 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	EPU

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-10-22
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.