8YWH | pdb_00008ywh

Cryo-EM structure of small and dead form SaCas9-RNA-DNA ternary complex (sdCas9)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Cas9 REC domain-like	8092302	3002580	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8092304	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8092304	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cas9 PI domain-like	8092305	3002581	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cas9 BH domain-like	8048680	3002579	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Lip_C	e8ywhA01	A: a/b three-layered sandwiches	X: ATP-grasp_6	H: ATP-grasp_6	T: ATP-grasp_6	F: Lip_C	ECOD (v294.1)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	sCas9 (Compact SaCas9)	DNA binding binding nucleic acid binding hydrolase activity catalytic activity endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid RNA binding cation binding ion binding metal ion binding small molecule binding	maintenance of CRISPR repeat elements chromosome organization primary metabolic process DNA metabolic process maintenance of DNA repeat elements nucleic acid metabolic process cellular component organization nucleobase-containing compound metabolic process organelle organization cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process biological process involved in interspecies interaction between organisms maintenance of CRISPR repeat elements chromosome organization primary metabolic process DNA metabolic process maintenance of DNA repeat elements nucleic acid metabolic process cellular component organization nucleobase-containing compound metabolic process organelle organization cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process 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	-
B	sgRNA	-	-	-
C	Target DNA	-	-	-
D	Non-target DNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR033114	Cas9-type HNH domain	Domain
A	IPR040555	Cas9, PI domain	Domain
A	IPR049473	CRISPR-associated endonuclease Cas9, PI domain, C-terminal domain	Domain
A	IPR055228	Cas9, RuvC domain	Domain
A	IPR028629	CRISPR-associated endonuclease Cas9	Family
A	IPR003615	HNH nuclease	Domain
A	IPR040656	Cas9, WED 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.