6JOO

Crystal structure of Corynebacterium diphtheriae Cas9 in complex with sgRNA and target DNA

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF18470	e6jooA1	A: alpha complex topology	X: CRISPR-associated endonuclease Cas9 alpha-helical lobe	H: CRISPR-associated endonuclease Cas9 alpha-helical lobe (From Topology)	T: CRISPR-associated endonuclease Cas9 alpha-helical lobe	F: PF18470	ECOD (1.6)
A	PF17894	e6jooA3	A: a+b two layers	X: SSHS domain	H: SSHS domain in CRISPR-associated endonuclease Cas9 (From Topology)	T: SSHS domain in CRISPR-associated endonuclease Cas9	F: PF17894	ECOD (1.6)
A	PF18525	e6jooA5	A: a+b complex topology	X: CRISPR-associated endonuclease Cas9 C-terminal domain (From Topology)	H: CRISPR-associated endonuclease Cas9 C-terminal domain (From Topology)	T: CRISPR-associated endonuclease Cas9 C-terminal domain	F: PF18525	ECOD (1.6)
A	PF17893	e6jooA4	A: a+b complex topology	X: CRISPR-associated endonuclease Cas9 beta-hairpin domain (From Topology)	H: CRISPR-associated endonuclease Cas9 beta-hairpin domain (From Topology)	T: CRISPR-associated endonuclease Cas9 beta-hairpin domain	F: PF17893	ECOD (1.6)
A	PF18541	e6jooA2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF18541	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF18470	Cas9 alpha-helical lobe domain (Cas9_a)	Cas9 alpha-helical lobe domain	This is an alpha-helical lobe domain found in Cas9 proteins. Cas9 enzymes adopt a bilobed architecture composed of a nuclease lobe containing juxtaposed RuvC and HNH nuclease domains and a variable alpha-helical lobe likely to be involved in nucleic ...	This is an alpha-helical lobe domain found in Cas9 proteins. Cas9 enzymes adopt a bilobed architecture composed of a nuclease lobe containing juxtaposed RuvC and HNH nuclease domains and a variable alpha-helical lobe likely to be involved in nucleic acid binding. Amino acid residues located in both the nuclease and alpha-helical lobe clefts are highly conserved within type II-A Cas9 proteins [1].	Domain
A	PF17893	CRISPR-associated endonuclease Cas9 beta-hairpin domain (Cas9_b_hairpin)	CRISPR-associated endonuclease Cas9 beta-hairpin domain	This is beta-hairpin domain found in Cas9 proteins from Actinobacteria. The beta-hairpin domain is not conserved in all type II-C Cas9 proteins. The beta-hairpin in Cas 9 from Streptococcus pyogenes blocks the HNH domain active site [1].	Domain
A	PF17894	Topo homolgy domain in CRISPR-associated endonuclease Cas9 (Cas9_Topo)	Topo homolgy domain in CRISPR-associated endonuclease Cas9	This is the Topo-homology domain found in Cas9 proteins from Actinobacteria. This domain bears structural similarity to a domain found in topoisomerase II [1].	Domain
A	PF18525	Cas9 C-terminal domain (Cas9_C)	Cas9 C-terminal domain	This is the C-terminal domain of Cas9 enzymes found in actinobacteria [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	CRISPR-associated protein,CRISPR-associated endonuclease Cas9	DNA binding binding organic cyclic compound binding nucleic acid binding endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding DNA binding binding organic cyclic compound binding nucleic acid binding endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding RNA binding	biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to virus defense response to other organism response to stress response to external biotic stimulus response to virus	-
B	Guide RNA	-	-	-
C [auth D]	Non-Target DNA	-	-	-
D [auth C]	Target DNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR040619	Cas9, alpha-helical lobe domain	Domain
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR041225	Cas9, topo homolgy domain	Domain
A	IPR033114	Cas9-type HNH domain	Domain
A	IPR040796	CRISPR-associated endonuclease Cas9, beta-hairpin domain	Domain
A	IPR041383	RuvC endonuclease subdomain 3	Domain
A	IPR003615	HNH nuclease	Domain
A	IPR002711	HNH endonuclease	Domain
A	IPR041217	Cas9 C-terminal domain	Domain

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 R01GM133198.