8JG9 | pdb_00008jg9

Cryo-EM structure of the SaCas9-sgRNA-AcrIIA15-promoter DNA dimer

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
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	His-Me finger endonucleases	8092303	3001893	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8092304	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cas9 BH domain-like	8048680	3002579	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cas9 PI domain-like	8092305	3002581	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Ribonuclease H-like	8092304	3000143	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Cas9 REC domain-like	8092302	3002580	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Cas9 BH domain-like	8048680	3002579	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Cas9 PI domain-like	8092305	3002581	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	His-Me finger endonucleases	8092303	3001893	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth D]	PF21574	CRISPR-associated endonuclease Cas9, C-terminal domain (Cas9_PI_C)	CRISPR-associated endonuclease Cas9, C-terminal domain	This domain is found at the C-terminal end of CRISPR-associated endonuclease Cas9 from Staphylococcus aureus (Cas9). This protein adopts a bilobed architecture consisting of a REC lobe and a NUC lobe connected by an arginine-rich bridge helix and a l ...	This domain is found at the C-terminal end of CRISPR-associated endonuclease Cas9 from Staphylococcus aureus (Cas9). This protein adopts a bilobed architecture consisting of a REC lobe and a NUC lobe connected by an arginine-rich bridge helix and a linker loop. The C-terminal region, known as the PI domain, can be divided into a Topoisomerase-homology (TOPO) domain (Pfam:PF18070) and a C- terminal domain (this entry). This domain forms a twisted six- stranded anti-parallel beta-sheet [1,2].	Domain
A, C [auth D]	PF13395	HNH endonuclease (HNH_4)	HNH endonuclease	This HNH nuclease domain is found in CRISPR-related proteins.	Domain
A, C [auth D]	PF18061	CRISPR-Cas9 WED domain (CRISPR_Cas9_WED)	CRISPR-Cas9 WED domain	This domain, known as the wedge (WED) domain, is found in Cas9 proteins which are present in Staphylococcus aureus. Cas9 cleaves double-stranded DNA targets with a protospacer adjacent motif (PAM) and complementarity to the guide RNA. The Cas9 WED do ...	This domain, known as the wedge (WED) domain, is found in Cas9 proteins which are present in Staphylococcus aureus. Cas9 cleaves double-stranded DNA targets with a protospacer adjacent motif (PAM) and complementarity to the guide RNA. The Cas9 WED domain has a fold comprising a twisted five-stranded beta sheet flanked by four alpha helices, and is responsible for the recognition of the distorted repeat: anti-repeat duplex. WED domains are responsible for the recognition of single-guide RNA scaffolds [1].	Domain
A, C [auth D]	PF22702	Cas9 RuvC domain (Cas9_RuvC)	Cas9 RuvC domain	This entry represent a RuvC endonuclease domain (RNAseH-like) domain found in CRISPR-Cas9 from Streptococcus pyogenes and related sequences [1-5]. This domain, and the HNH (Pfam:PF13395) domain of Cas9, are used to cleave the DNA strands complementar ...	This entry represent a RuvC endonuclease domain (RNAseH-like) domain found in CRISPR-Cas9 from Streptococcus pyogenes and related sequences [1-5]. This domain, and the HNH (Pfam:PF13395) domain of Cas9, are used to cleave the DNA strands complementary (target) and non-complementary (non-target) to the crRNA, respectively [5]. This domain is related to Pfam:PF18541.	Domain
A, C [auth D]	PF18070	CRISPR-Cas9 PI domain (Cas9_PI2)	CRISPR-Cas9 PI domain	This domain is found in Cas9 proteins which can be Staphylococcus aureus. Cas9 cleaves double-stranded DNA targets with a protospacer adjacent motif (PAM) and complementarity to the guide RNA. When this domain is combined with the C-terminal domain i ...	This domain is found in Cas9 proteins which can be Staphylococcus aureus. Cas9 cleaves double-stranded DNA targets with a protospacer adjacent motif (PAM) and complementarity to the guide RNA. When this domain is combined with the C-terminal domain it is called the Pam-interacting (PI) domain. The Cas9 orthologs from different microbes have highly divergent sequences but their PI domains share a conserved core fold and recognize distinct PAM sequences [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth D]	CRISPR-associated endonuclease Cas9	DNA binding binding nucleic acid binding endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity 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 response to stimulus response to other organism defense response 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, D [auth E]	sgRNA	-	-	-
E [auth F], H [auth C]	AcrIIA15	-	-	-
F [auth G]	DNA (25-MER)	-	-	-
G [auth H]	DNA (25-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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