4OGC | pdb_00004ogc

Crystal structure of the Type II-C Cas9 enzyme from Actinomyces naeslundii

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4ogca1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	RuvC-like domain from CRISPR-associated protein Cas9	CRISPR-associated endonuclease Cas9/Csn1, RuvC-like domain	(Actinomyces naeslundii str. Howell 279 ) [TaxId: 1115803 ],	SCOPe (2.08)
A	d4ogca2	Alpha and beta proteins (a+b)	His-Me finger endonucleases	His-Me finger endonucleases	HNH domain from CRISPR-associated protein Cas9	CRISPR-associated endonuclease Cas9/Csn1, HNH domain	(Actinomyces naeslundii str. Howell 279 ) [TaxId: 1115803 ],	SCOPe (2.08)
A	d4ogca3	Alpha and beta proteins (a+b)	CRISPR-associated endonuclease Cas9/Csn1, Target recognition (REC) lobe	CRISPR-associated endonuclease Cas9/Csn1, Target recognition (REC) lobe	CRISPR-associated endonuclease Cas9/Csn1, Target recognition (REC) lobe	CRISPR-associated endonuclease Cas9/Csn1, REC lobe	(Actinomyces naeslundii str. Howell 279 ) [TaxId: 1115803 ],	SCOPe (2.08)
A	d4ogca4	Multi-domain proteins (alpha and beta)	CRISPR-associated endonuclease Cas9/Csn1, Protospace-adjacent motif (PAM)-interacting domain	CRISPR-associated endonuclease Cas9/Csn1, PAM-interacting (PI) domain	CRISPR-associated endonuclease Cas9/Csn1, PAM-interacting (PI) domain	CRISPR-associated endonuclease Cas9/Csn1, PI domain	(Actinomyces naeslundii str. Howell 279 ) [TaxId: 1115803 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e4ogcA1	A: CRISPR-associated endonuclease Cas9 C-terminal domain	X: CRISPR-associated endonuclease Cas9 C-terminal domain	H: CRISPR-associated endonuclease Cas9 C-terminal domain	T: Cas9_a	F:	ECOD (20:10:01)
A		e4ogcA2	A: CRISPR-associated endonuclease Cas9 C-terminal domain	X: CRISPR-associated endonuclease Cas9 C-terminal domain	H: CRISPR-associated endonuclease Cas9 C-terminal domain	T: HNH	F:	ECOD (20:10:01)
A		e4ogcA4	A: CRISPR-associated endonuclease Cas9 C-terminal domain	X: CRISPR-associated endonuclease Cas9 C-terminal domain	H: CRISPR-associated endonuclease Cas9 C-terminal domain	T: Cas9_Topo	F:	ECOD (20:10:01)
A		e4ogcA5	A: CRISPR-associated endonuclease Cas9 C-terminal domain	X: CRISPR-associated endonuclease Cas9 C-terminal domain	H: CRISPR-associated endonuclease Cas9 C-terminal domain	T: Cas9_C	F:	ECOD (20:10:01)
A		e4ogcA6	A: CRISPR-associated endonuclease Cas9 beta-hairpin domain	X: CRISPR-associated endonuclease Cas9 beta-hairpin domain	H: CRISPR-associated endonuclease Cas9 beta-hairpin domain	T: Cas9_b_hairpin	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	3.30.70.3520	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	HNH endonuclease domain protein	DNA binding binding nucleic acid binding hydrolase activity catalytic activity endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA binding binding nucleic acid binding hydrolase activity catalytic activity endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid 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 defense response to virus response to stimulus defense response response to other organism response to stress response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus	-

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	IPR028629	CRISPR-associated endonuclease Cas9	Family
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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.