2F8S | pdb_00002f8s

Crystal structure of Aa-Ago with externally-bound siRNA

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)
D [auth B]	d2f8sb1	All beta proteins	SH3-like barrel	PAZ domain	PAZ domain	automated matches	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
D [auth B]	d2f8sb3	Alpha and beta proteins (a/b)	Phosphotyrosine protein phosphatases I-like	PIWI domain N-terminal-like	PIWI domain N-terminal	Argonaute homologue Aq_1447	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
D [auth B]	d2f8sb4	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	PIWI domain C-terminal	Argonaute homologue Aq_1447	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
C [auth A]	d2f8sa1	All beta proteins	SH3-like barrel	PAZ domain	PAZ domain	automated matches	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
C [auth A]	d2f8sa3	Alpha and beta proteins (a/b)	Phosphotyrosine protein phosphatases I-like	PIWI domain N-terminal-like	PIWI domain N-terminal	Argonaute homologue Aq_1447	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
C [auth A]	d2f8sa4	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	PIWI domain C-terminal	Argonaute homologue Aq_1447	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth B]	SCOP2B Superfamily	PAZ domain	8034965	3001750	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Ribonuclease H-like	8034967	3000143	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	RNA-binding domain, RBD	8053612	3000110	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Mid domain of argonaute	8053613	3002210	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	PAZ domain	8034965	3001750	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Mid domain of argonaute	8053613	3002210	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	RNA-binding domain, RBD	8053612	3000110	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Ribonuclease H-like	8034967	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)
D [auth B]	COG1431_3rd_1	e2f8sB4	A: beta barrels	X: SH3	H: SH3	T: SH3	F: COG1431_3rd_1	ECOD (1.6)
D [auth B]	COG1431_1st_1	e2f8sB5	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: COG1431_1st_1	ECOD (1.6)
D [auth B]	COG1431_2nd	e2f8sB6	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: COG1431_2nd	ECOD (1.6)
D [auth B]	Piwi_N	e2f8sB2	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: Piwi_N	ECOD (1.6)
D [auth B]	Piwi_C_1	e2f8sB3	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)
C [auth A]	COG1431_3rd_1	e2f8sA4	A: beta barrels	X: SH3	H: SH3	T: SH3	F: COG1431_3rd_1	ECOD (1.6)
C [auth A]	COG1431_1st_1	e2f8sA5	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: COG1431_1st_1	ECOD (1.6)
C [auth A]	COG1431_2nd	e2f8sA6	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: COG1431_2nd	ECOD (1.6)
C [auth A]	Piwi_N	e2f8sA2	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: Piwi_N	ECOD (1.6)
C [auth A]	Piwi_C_1	e2f8sA3	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)
D [auth B]	2.30.340.10	Mainly Beta	Roll	PAZ domain fold	PAZ domain superfamily	CATH (4.3.0)
D [auth B]	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
D [auth B]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
C [auth A]	2.30.340.10	Mainly Beta	Roll	PAZ domain fold	PAZ domain superfamily	CATH (4.3.0)
C [auth A]	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
C [auth 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
C [auth A], D [auth B]	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
C [auth A], D [auth B]	PF22430	Ago, N-terminal domain (Aa-Ago_N)	Ago, N-terminal domain	This entry represents the N-terminal domain of Argonaute (Ago) from Aquifex aeolicus. This domain is composed of an antiparallel five-stranded beta sheet core that has one alpha helix positioned along one face of the sheet. Ago use short ssDNA sequen ...	This entry represents the N-terminal domain of Argonaute (Ago) from Aquifex aeolicus. This domain is composed of an antiparallel five-stranded beta sheet core that has one alpha helix positioned along one face of the sheet. Ago use short ssDNA sequences as guides (gDNA) to bind complementary target strands, resulting in cleavage of the target RNA [1,2].	Domain
C [auth A], D [auth B]	PF18349	PAZ domain (PAZ_4)	PAZ domain	This is a Paz domain found in Argonaute proteins from Aquifex aeolicus bacteria. The PAZ core fold in Aquifex aeolicus bacteria Ago (Aa-Ago) proteins is closely related to the human hAgo1 PAZ domain [1]. Structural and functional studies of Aa-Ago in ...	This is a Paz domain found in Argonaute proteins from Aquifex aeolicus bacteria. The PAZ core fold in Aquifex aeolicus bacteria Ago (Aa-Ago) proteins is closely related to the human hAgo1 PAZ domain [1]. Structural and functional studies of Aa-Ago indicate that conformational rearrangement of the PAZ domain may be critical for the catalytic cycle of Argonaute and the RNA-induced silencing complex [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth A], D [auth B]	Argonaute protein	DNA binding binding nucleic acid binding endonuclease activity nuclease activity catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity RNA binding cation binding ion binding metal ion binding DNA binding binding nucleic acid binding endonuclease activity nuclease activity catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity RNA binding cation binding ion binding metal ion binding small molecule binding	-	-
A [auth C], B [auth D]	5'-R(PAPGPAPCPAPGPCPAPUPAPUPAPUPGPCPUPGPUPCPUPUPU)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth B]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR036085	PAZ domain superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR003165	Piwi domain	Domain
C [auth A], D [auth B]	IPR041659	Paz_1	Unknown
C [auth A], D [auth B]	IPR003100	PAZ domain	Domain
C [auth A], D [auth B]	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.