Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyCas9 BH domain-like8048680 3002579 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyCas9 PI domain-like8092305 3002581 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyRibonuclease H-like8092304 3000143 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyCas9 REC domain-like8092302 3002580 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyRibonuclease H-like8092304 3000143 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyRibonuclease H-like8092304 3000143 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyHis-Me finger endonucleases8092303 3001893 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
APF16592e7vw3A5 A: alpha complex topologyX: CRISPR-associated endonuclease Cas9 alpha-helical lobeH: CRISPR-associated endonuclease Cas9 alpha-helical lobe (From Topology)T: CRISPR-associated endonuclease Cas9 alpha-helical lobeF: PF16592ECOD (1.6)
APF18070e7vw3A2 A: a+b two layersX: SSHS domainH: SSHS domain in CRISPR-associated endonuclease Cas9 (From Topology)T: SSHS domain in CRISPR-associated endonuclease Cas9F: PF18070ECOD (1.6)
APF21574e7vw3A1 A: a+b complex topologyX: 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 domainF: PF21574ECOD (1.6)
APF18061e7vw3A6 A: a+b complex topologyX: CRISPR-associated endonuclease Cas9 wedge domain (From Topology)H: CRISPR-associated endonuclease Cas9 wedge domain (From Topology)T: CRISPR-associated endonuclease Cas9 wedge domainF: PF18061ECOD (1.6)
APF22702e7vw3A4 A: mixed a+b and a/bX: Ribonuclease H-likeH: Ribonuclease H-like (From Topology)T: Ribonuclease H-likeF: PF22702ECOD (1.6)
APF13395e7vw3A3 A: few secondary structure elementsX: His-Me finger endonucleases (From Homology)H: His-Me finger endonucleasesT: His-Me finger endonucleasesF: PF13395ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF21574CRISPR-associated endonuclease Cas9, C-terminal domain (Cas9_PI_C)CRISPR-associated endonuclease Cas9, C-terminal domainThis 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
PF13395HNH endonuclease (HNH_4)HNH endonucleaseThis HNH nuclease domain is found in CRISPR-related proteins.Domain
PF18541RuvC endonuclease subdomain 3 (RuvC_III)RuvC endonuclease subdomain 3Cas9 proteins are abundant across the bacterial kingdom, but vary widely in both sequence and size. All known Cas9 enzymes contain an HNH domain that cleaves the DNA strand complementary to the guide RNA sequence (target strand), and a RuvC nuclease ...Cas9 proteins are abundant across the bacterial kingdom, but vary widely in both sequence and size. All known Cas9 enzymes contain an HNH domain that cleaves the DNA strand complementary to the guide RNA sequence (target strand), and a RuvC nuclease domain required for cleaving the noncomplementary strand (non-target strand), yielding double-strand DNA breaks (DSBs). The crystal structures of type II-A and II-C Cas9 proteins highlight the features in Cas9 enzymes that support their function as RNA-guided endonucleases. 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. The RuvC domain forms the structural core of the nuclease lobe, a six-stranded beta sheet surrounded by four alpha helices, with all three conserved subdomains (I, II, III) contributing catalytic residues to the active site [1].
Domain
PF18061CRISPR-Cas9 WED domain (CRISPR_Cas9_WED)CRISPR-Cas9 WED domainThis 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
PF18070CRISPR-Cas9 PI domain (Cas9_PI2)CRISPR-Cas9 PI domainThis 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

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Target DNA strand---
CRISPR-associated endonuclease Cas9 -
single-guide RNA---
Non-target DNA strand---