9AR4

CryoEM structure of ThermoCas9 in post-cleavage state bound with the DNA containing NNNNCCA PAM

PDB DOI: https://doi.org/10.2210/pdb9AR4/pdb
EM Map EMD-43769: EMDB EMDataResource
NAKB: 9AR4

Classification: DNA BINDING PROTEIN/DNA/RNA
Organism(s): Geobacillus thermodenitrificans, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-02-22 Released: 2025-02-26
Deposition Author(s): Shu, Y., Zhao, Y., Li, H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.20 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

Molecular Basis for Epigenetic-sensitive Editing by Cas9

Roth, M., Shu, Y., Trasanidis, D., Zhao, Y., Hoffman, R., van der Oost, J., Li, H.

To be published.

Macromolecule Content

Total Structure Weight: 192.98 kDa
Atom Count: 12,261
Modelled Residue Count: 1,200
Deposited Residue Count: 1,290
Unique protein chains: 1
Unique nucleic acid chains: 5

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas9	F [auth A]	1,082	Geobacillus thermodenitrificans	Mutation(s): 0 Gene Names: cas9-2, cas9, GTHT12_03401 EC: 3.1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Single guide RNA	A [auth B]	149	Geobacillus thermodenitrificans
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Cleaved 3' target DNA strand	B [auth C]	26	synthetic construct
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 3
Molecule	Chains	Length	Organism	Image
Cleaved 3' non-target DNA strand	C [auth D]	14	synthetic construct
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 4
Molecule	Chains	Length	Organism	Image
Cleaved 5' target DNA strand	D [auth P]	14	synthetic construct
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 5
Molecule	Chains	Length	Organism	Image
Cleaved 5' non-target DNA strand	E [auth X]	5	synthetic construct
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP (Subject of Investigation/LOI) Query on GTP Download Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	G [auth B] H [auth B] J [auth A] K [auth A] L [auth A] G [auth B], H [auth B], J [auth A], K [auth A], L [auth A], M [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]