5AXW | pdb_00005axw

Crystal structure of Staphylococcus aureus Cas9 in complex with sgRNA and target DNA (TTGGGT PAM)

External Resource: Annotation

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5axwa1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	RuvC-like domain from CRISPR-associated protein Cas9	CRISPR-associated endonuclease Cas9/Csn1, RuvC-like domain	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
A	d5axwa2	Alpha and beta proteins (a+b)	His-Me finger endonucleases	His-Me finger endonucleases	HNH domain from CRISPR-associated protein Cas9	CRISPR-associated endonuclease Cas9/Csn1, HNH domain	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
A	d5axwa3	Alpha and beta proteins (a+b)	CRISPR-associated endonuclease Cas9/Csn1, Target recognition (REC) lobe	CRISPR-associated endonuclease Cas9/Csn1, Target recognition (REC) lobe	CRISPR-associated endonuclease Cas9/Csn1, Target recognition (REC) lobe	CRISPR-associated endonuclease Cas9/Csn1, REC lobe	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
A	d5axwa4	Multi-domain proteins (alpha and beta)	CRISPR-associated endonuclease Cas9/Csn1, Protospace-adjacent motif (PAM)-interacting domain	CRISPR-associated endonuclease Cas9/Csn1, PAM-interacting (PI) domain	CRISPR-associated endonuclease Cas9/Csn1, PAM-interacting (PI) domain	CRISPR-associated endonuclease Cas9/Csn1, PI domain	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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	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	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 REC domain-like	8092302	3002580	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	e5axwA1	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	UNK_F_TYPE	e5axwA4	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: UNK_F_TYPE	ECOD (1.6)
A	EUF08578	e5axwA5	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: EUF08578	ECOD (1.6)
A	EUF08585	e5axwA6	A: a+b complex topology	X: CRISPR-associated endonuclease Cas9 wedge domain (From Topology)	H: CRISPR-associated endonuclease Cas9 wedge domain (From Topology)	T: CRISPR-associated endonuclease Cas9 wedge domain	F: EUF08585	ECOD (1.6)
A	Cas9_1st	e5axwA2	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)
A	HNH_4	e5axwA3	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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	DNA (5'-D(TPTPGPGPGPTPAPG)-3')	-	-	-
C	DNA (28-MER)	-	-	-
B	RNA (73-MER)	-	-	-
A	CRISPR-associated endonuclease Cas9	DNA binding binding nucleic acid binding endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid 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 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	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.