6O0X | pdb_00006o0x

Conformational states of Cas9-sgRNA-DNA ternary complex in the presence of magnesium

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD 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 BH domain-like	8045840	3002579	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8092300	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cas9 REC domain-like	8045843	3002580	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8092300	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cas9 PI domain-like	8092301	3002581	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	Cas9_REC	e6o0xA1	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: Cas9_REC	ECOD (1.6)
A	Cas9_PI_N	e6o0xA4	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: Cas9_PI_N	ECOD (1.6)
A	Cas9_PI_C	e6o0xA2	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: Cas9_PI_C	ECOD (1.6)
A	Cas9_1st	e6o0xA3	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Cas9_1st	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF16592	REC lobe of CRISPR-associated endonuclease Cas9 (Cas9_REC)	REC lobe of CRISPR-associated endonuclease Cas9	-	Family
A	PF16593	Bridge helix of CRISPR-associated endonuclease Cas9 (Cas9-BH)	Bridge helix of CRISPR-associated endonuclease Cas9	-	Family
A	PF16595	PAM-interacting domain of CRISPR-associated endonuclease Cas9 (Cas9_PI)	PAM-interacting domain of CRISPR-associated endonuclease Cas9	Cas9_PI is a family found at the C-terminal of bacterial type II CRISPR system Cas9 endonuclease. This domain adopts a novel protein fold that is unique to the Cas9 family. It is positioned in the structure-DNA-complex to recognise the PAM sequence o ...	Cas9_PI is a family found at the C-terminal of bacterial type II CRISPR system Cas9 endonuclease. This domain adopts a novel protein fold that is unique to the Cas9 family. It is positioned in the structure-DNA-complex to recognise the PAM sequence on the non-complementary DNA strand of the crRNA. PAM sequence is protospacer-adjacent motifs on DNA. See family CRISPR-DR2, Rfam:RF01315. Cas9 carries two nuclease domains, HNH and RuvC, which cleave the DNA strands that are complementary and non-complementary to the 20 nucleotide guide sequence in crRNAs, respectively [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth c]	3' product of target strand DNA	-	-	-
D	non-target strand DNA	-	-	-
C	5' product of target strand DNA	-	-	-
B	single guide RNA	-	-	-
A	CRISPR-associated endonuclease Cas9/Csn1	DNA binding binding nucleic acid binding hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA DNA nuclease activity DNA binding binding nucleic acid binding hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA DNA nuclease 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 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	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR032240	CRISPR-associated endonuclease Cas9, REC lobe	Domain
A	IPR032239	CRISPR-associated endonuclease Cas9, bridge helix	Domain
A	IPR033114	Cas9-type HNH domain	Domain
A	IPR055228	Cas9, RuvC domain	Domain
A	IPR028629	CRISPR-associated endonuclease Cas9	Family
A	IPR003615	HNH nuclease	Domain
A	IPR032237	CRISPR-associated endonuclease Cas9, PAM-interacting 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.