2F8S

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
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)
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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], D [auth B]	PF02171	Piwi domain (Piwi)	Piwi domain	-	Family
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
A [auth C], B [auth D]	5'-R(PAPGPAPCPAPGPCPAPUPAPUPAPUPGPCPUPGPUPCPUPUPU)-3'	-	-	-
C [auth A], D [auth B]	Argonaute protein	DNA binding binding organic cyclic compound binding nucleic acid binding endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity RNA binding DNA binding binding organic cyclic compound binding nucleic acid binding endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity RNA binding cation binding ion binding metal ion binding small molecule binding	-	-

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]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR041659	Argonaute, PAZ domain, Aquifex	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.