6JE4

Crystal structure of Nme1Cas9-sgRNA-dsDNA dimer mediated by double protein inhibitor AcrIIC3 monomers

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
K	Cas9_REC	e6je4K2	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)
K	Cas9_2nd	e6je4K3	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_2nd	ECOD (1.6)
K	UNK_F_TYPE	e6je4K4	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: UNK_F_TYPE	ECOD (1.6)
K	UvrD_C	e6je4K5	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: UvrD_C	ECOD (1.6)
K	Cas9_1st	e6je4K6	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)
K	HNH_4	e6je4K1	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)
O	Cas9_REC	e6je4O1	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)
O	Cas9_2nd	e6je4O6	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_2nd	ECOD (1.6)
O	UNK_F_TYPE	e6je4O5	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: UNK_F_TYPE	ECOD (1.6)
O	UvrD_C	e6je4O4	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: UvrD_C	ECOD (1.6)
O	Cas9_1st	e6je4O2	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)
O	HNH_4	e6je4O3	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
A, F [auth E], K, O	PF13395	HNH endonuclease (HNH_4)	HNH endonuclease	This HNH nuclease domain is found in CRISPR-related proteins.	Domain
A, F [auth E], K, O	PF18541	RuvC endonuclease subdomain 3 (RuvC_III)	RuvC endonuclease subdomain 3	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 ...	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, F [auth E], K, O	CRISPR-associated endonuclease Cas9	DNA binding binding organic cyclic compound 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	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 maintenance of CRISPR repeat elements chromosome organization 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 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	-
B [auth C], G, L [auth M], P [auth Q]	target DNA strand	-	-	-
C [auth D], H, M [auth N], Q [auth R]	non-target DNA strand	-	-	-
D [auth B], I [auth F], N [auth L], R [auth P]	sgRNA	-	-	-
E [auth I], J, S, T	AcrIIC3	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, F [auth E], K, O	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, F [auth E], K, O	IPR041383	RuvC endonuclease subdomain 3	Domain
A, F [auth E], K, O	IPR028629	CRISPR-associated endonuclease Cas9	Family
A, F [auth E], K, O	IPR033114	Cas9-type HNH domain	Domain
A, F [auth E], K, O	IPR003615	HNH nuclease	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.