5B2R

Crystal structure of the Streptococcus pyogenes Cas9 VQR variant in complex with sgRNA and target DNA (TGA PAM)

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)
B	SCOP2 Family	Cas9-like	8045838	4004716	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Cas9 BH domain-like	8045840	3002579	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Cas9 REC domain-like	8045843	3002580	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	His-Me finger endonucleases	8048679	3001893	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Ribonuclease H-like	8092300	3000143	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Cas9 PI domain-like	8092301	3002581	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Cas9_REC	e5b2rB4	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)
B	Cas9_PI_N	e5b2rB3	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)
B	Cas9_PI_C	e5b2rB5	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)
B	Cas9_1st	e5b2rB1	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)
B	HNH_4	e5b2rB2	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: HNH_4	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF16593	Bridge helix of CRISPR-associated endonuclease Cas9 (Cas9-BH)	Bridge helix of CRISPR-associated endonuclease Cas9	-	Family
B	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
B	PF13395	HNH endonuclease (HNH_4)	HNH endonuclease	This HNH nuclease domain is found in CRISPR-related proteins.	Domain
B	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Guide RNA	-	-	-
B	CRISPR-associated endonuclease Cas9	DNA binding binding organic cyclic compound binding nucleic acid binding nuclease activity hydrolase activity, acting on ester bonds 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid DNA binding binding organic cyclic compound binding nucleic acid binding nuclease activity hydrolase activity, acting on ester bonds 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid 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 response to stimulus response to other organism defense response defense response to symbiont 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	-
C	Target DNA	-	-	-
D	Non-target DNA, DNA (5'-D(TPGPAPGPAPTPTPG)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
B	IPR032240	CRISPR-associated endonuclease Cas9, REC lobe	Domain
B	IPR032239	CRISPR-associated endonuclease Cas9, bridge helix	Domain
B	IPR033114	Cas9-type HNH domain	Domain
B	IPR028629	CRISPR-associated endonuclease Cas9	Family
B	IPR003615	HNH nuclease	Domain
B	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.