4QQY

Crystal structure of T. fusca Cas3-ADP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
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)
E	d4qqye1	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	HD domain from Cas3-like	CRISPR-associated protein Cas3	(Thermobifida fusca YX ) [TaxId: 269800 ],	SCOPe (2.08)
E	d4qqye2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	CRISPR-associated protein Cas3	(Thermobifida fusca YX ) [TaxId: 269800 ],	SCOPe (2.08)
E	d4qqye4	Alpha and beta proteins (a+b)	Cas3 C-terminal domain-like	Cas3 C-terminal domain-like	Cas3 C-terminal domain-like	CRISPR-associated protein Cas3	(Thermobifida fusca YX ) [TaxId: 269800 ],	SCOPe (2.08)
A	d4qqya1	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	HD domain from Cas3-like	CRISPR-associated protein Cas3	(Thermobifida fusca YX ) [TaxId: 269800 ],	SCOPe (2.08)
A	d4qqya2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	CRISPR-associated protein Cas3	(Thermobifida fusca YX ) [TaxId: 269800 ],	SCOPe (2.08)
A	d4qqya4	Alpha and beta proteins (a+b)	Cas3 C-terminal domain-like	Cas3 C-terminal domain-like	Cas3 C-terminal domain-like	CRISPR-associated protein Cas3	(Thermobifida fusca YX ) [TaxId: 269800 ],	SCOPe (2.08)
C	d4qqyc1	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	HD domain from Cas3-like	CRISPR-associated protein Cas3	(Thermobifida fusca YX ) [TaxId: 269800 ],	SCOPe (2.08)
C	d4qqyc2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	CRISPR-associated protein Cas3	(Thermobifida fusca YX ) [TaxId: 269800 ],	SCOPe (2.08)
C	d4qqyc4	Alpha and beta proteins (a+b)	Cas3 C-terminal domain-like	Cas3 C-terminal domain-like	Cas3 C-terminal domain-like	CRISPR-associated protein Cas3	(Thermobifida fusca YX ) [TaxId: 269800 ],	SCOPe (2.08)
G	d4qqyg1	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	HD domain from Cas3-like	CRISPR-associated protein Cas3	(Thermobifida fusca YX ) [TaxId: 269800 ],	SCOPe (2.08)
G	d4qqyg2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	CRISPR-associated protein Cas3	(Thermobifida fusca YX ) [TaxId: 269800 ],	SCOPe (2.08)
G	d4qqyg4	Alpha and beta proteins (a+b)	Cas3 C-terminal domain-like	Cas3 C-terminal domain-like	Cas3 C-terminal domain-like	CRISPR-associated protein Cas3	(Thermobifida fusca YX ) [TaxId: 269800 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E	PF18019	e4qqyE2	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: PF18019	ECOD (1.6)
E	F_UNCLASSIFIED	e4qqyE4	A: a+b two layers	X: Cas3 C-terminal domain	H: Cas3 C-terminal domain (From Topology)	T: Cas3 C-terminal domain	F: F_UNCLASSIFIED	ECOD (1.6)
E	F_UNCLASSIFIED	e4qqyE3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: F_UNCLASSIFIED	ECOD (1.6)
E	PF22590	e4qqyE1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF22590	ECOD (1.6)
A	PF18019	e4qqyA2	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: PF18019	ECOD (1.6)
A	F_UNCLASSIFIED	e4qqyA4	A: a+b two layers	X: Cas3 C-terminal domain	H: Cas3 C-terminal domain (From Topology)	T: Cas3 C-terminal domain	F: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e4qqyA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF22590	e4qqyA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF22590	ECOD (1.6)
C	PF18019	e4qqyC2	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: PF18019	ECOD (1.6)
C	F_UNCLASSIFIED	e4qqyC4	A: a+b two layers	X: Cas3 C-terminal domain	H: Cas3 C-terminal domain (From Topology)	T: Cas3 C-terminal domain	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e4qqyC3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: F_UNCLASSIFIED	ECOD (1.6)
C	PF22590	e4qqyC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF22590	ECOD (1.6)
G	PF18019	e4qqyG2	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: PF18019	ECOD (1.6)
G	F_UNCLASSIFIED	e4qqyG4	A: a+b two layers	X: Cas3 C-terminal domain	H: Cas3 C-terminal domain (From Topology)	T: Cas3 C-terminal domain	F: F_UNCLASSIFIED	ECOD (1.6)
G	F_UNCLASSIFIED	e4qqyG3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: F_UNCLASSIFIED	ECOD (1.6)
G	PF22590	e4qqyG1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF22590	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	1.10.3210.30	Mainly Alpha	Orthogonal Bundle	Hypothetical protein af1432		CATH (4.3.0)
A	1.10.3210.30	Mainly Alpha	Orthogonal Bundle	Hypothetical protein af1432		CATH (4.3.0)
C	1.10.3210.30	Mainly Alpha	Orthogonal Bundle	Hypothetical protein af1432		CATH (4.3.0)
G	1.10.3210.30	Mainly Alpha	Orthogonal Bundle	Hypothetical protein af1432		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	PF18395	Cas3 C-terminal domain (Cas3_C)	Cas3 C-terminal domain	This is the C-temrinal domain of Cas3 proteins. The C-terminal domain (CTD) is shown to completely wrap ssDNA inside the helicase. Deletion of the CTD (aa 819-924) reduced CRISPR interference. It is suggested that the CTD regulates the N-terminal ...	This is the C-temrinal domain of Cas3 proteins. The C-terminal domain (CTD) is shown to completely wrap ssDNA inside the helicase. Deletion of the CTD (aa 819-924) reduced CRISPR interference. It is suggested that the CTD regulates the N-terminal HD nuclease activity by functioning as a substrate filter [1].	Domain
A, C, E, G	PF18019	Cas3, HD domain (Cas3_HD)	Cas3, HD domain	This HD domain is found at the N-terminus of Cas3 enzymes fused to a helicase domain. This domain is sometimes found as a separate protein. It acts as a nuclease that cleaves ssDNA.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	CRISPR-associated helicase, Cas3 family	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity hydrolase activity cation binding metal ion 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	-
B, D, F, H	HD nuclease	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR006474	Helicase Cas3, CRISPR-associated, core	Domain
A, C, E, G	IPR041372	Cas3, C-terminal	Domain
A, C, E, G	IPR001650	Helicase, C-terminal domain-like	Domain
A, C, E, G	IPR038257	CRISPR-associated Cas3-type HD domain superfamily	Homologous Superfamily
A, C, E, G	IPR006483	CRISPR-associated Cas3-type, HD domain	Domain
A, C, E, G	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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 R01GM133198.