1Z26 | pdb_00001z26

Structure of Pyrococcus furiosus Argonaute with bound tungstate

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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)
A	d1z26a1	All beta proteins	SH3-like barrel	PAZ domain	PAZ domain	Argonaute homologue PF0537	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
A	d1z26a3	Alpha and beta proteins (a/b)	Phosphotyrosine protein phosphatases I-like	PIWI domain N-terminal-like	PIWI domain N-terminal	Argonaute homologue PF0537	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
A	d1z26a4	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	PIWI domain C-terminal	Argonaute homologue PF0537	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
A	d1z26a5	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	RNA-binding domain, RBD	8091463	3000110	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Mid domain of argonaute	8091464	3002210	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PAZ domain	8040607	3001750	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8040608	3000143	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	PAZ_siRNAbind	e1z26A1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PAZ_siRNAbind	ECOD (1.6)
A	EUF08366	e1z26A4	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: EUF08366	ECOD (1.6)
A	EUF08367	e1z26A3	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: EUF08367	ECOD (1.6)
A	COG1431_4th	e1z26A2	A: a/b three-layered sandwiches	X: Middle domain in Argonaute homologs (From Topology)	H: Middle domain in Argonaute homologs (From Topology)	T: Middle domain in Argonaute homologs	F: COG1431_4th	ECOD (1.6)
A	Piwi_C_1	e1z26A5	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Piwi_C_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.70.180	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
A	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF22476	Argonaute, N-terminal domain (Ago_N_3)	Argonaute, N-terminal domain	This domain is found at the N-terminal end of Protein argonaute from Pyrococcus furiosus (Ago), a component of the RNAi effector complex (RISC). Ago is organised into four domains: N (this entry), PAZ (Pfam:PF12212), middle and PIWI (Pfam:PF02171). T ...	This domain is found at the N-terminal end of Protein argonaute from Pyrococcus furiosus (Ago), a component of the RNAi effector complex (RISC). Ago is organised into four domains: N (this entry), PAZ (Pfam:PF12212), middle and PIWI (Pfam:PF02171). This domain shows a small four-stranded beta-sheet, three alpha-helices and a beta-hairpin [1].	Domain
A	PF02171	Piwi domain (Piwi)	Piwi domain	This domain is found in the protein Piwi and its relatives. The function of this domain is the dsRNA guided hydrolysis of ssRNA. Determination of the crystal structure of Argonaute reveals that PIWI is an RNase H domain, and identifies Argonaute as S ...	This domain is found in the protein Piwi and its relatives. The function of this domain is the dsRNA guided hydrolysis of ssRNA. Determination of the crystal structure of Argonaute reveals that PIWI is an RNase H domain, and identifies Argonaute as Slicer, the enzyme that cleaves mRNA in the RNAi RISC complex [2]. In addition, Mg+2 dependence and production of 3'-OH and 5' phosphate products are shared characteristics of RNaseH and RISC. The PIWI domain core has a tertiary structure belonging to the RNase H family of enzymes. RNase H fold proteins all have a five-stranded mixed beta-sheet surrounded by helices. By analogy to RNase H enzymes which cleave single-stranded RNA guided by the DNA strand in an RNA/DNA hybrid, the PIWI domain can be inferred to cleave single-stranded RNA, for example mRNA, guided by double stranded siRNA.	Domain
A	PF12212	PAZ domain (PAZ_2)	PAZ domain	This entry corresponds to the PAZ domain found in some archaeal argonaute proteins [1]. It is an siRNA binding domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Argonaute	DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid catalytic activity DNA nuclease activity DNA binding binding nucleic acid binding cation binding manganese ion binding transition metal ion binding ion binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid catalytic activity DNA nuclease activity DNA binding binding nucleic acid binding cation binding manganese ion binding transition metal ion binding ion binding metal ion binding small molecule binding RNA 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 clearance of foreign intracellular DNA clearance of foreign intracellular nucleic acids response to biotic stimulus defense response to other organism response to stress response to external biotic stimulus	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR055253	Argonaute, N-terminal domain, thermococcales	Domain
A	IPR021103	Argonaute PAZ domain, archaea	Domain
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR036085	PAZ domain superfamily	Homologous Superfamily
A	IPR003165	Piwi domain	Domain
A	IPR003100	PAZ domain	Domain
A	IPR012337	Ribonuclease H-like superfamily	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 R01GM157729.