5XQ2 | pdb_00005xq2

Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 5A6 on the guide strand

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ribonuclease H-like	8053637	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RNA-binding domain, RBD	8053634	3000110	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PAZ domain	8053635	3001750	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Mid domain of argonaute	8053636	3002210	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	Mid domain of argonaute	8053636	3002210	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	RNA-binding domain, RBD	8053634	3000110	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	Ribonuclease H-like	8053637	3000143	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	PAZ domain	8053635	3001750	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	EUF07576	e5xq2A4	A: beta barrels	X: SH3	H: SH3	T: SH3	F: EUF07576	ECOD (1.6)
A	EUF08364	e5xq2A3	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: EUF08364	ECOD (1.6)
A	EUF08368	e5xq2A5	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: EUF08368	ECOD (1.6)
A	Piwi_piwi-like_ProArk	e5xq2A6	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_piwi-like_ProArk	ECOD (1.6)
A	Piwi_C_1	e5xq2A1	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)
E [auth B]	EUF07576	e5xq2B4	A: beta barrels	X: SH3	H: SH3	T: SH3	F: EUF07576	ECOD (1.6)
E [auth B]	EUF08364	e5xq2B3	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: EUF08364	ECOD (1.6)
E [auth B]	EUF08368	e5xq2B2	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: EUF08368	ECOD (1.6)
E [auth B]	Piwi_piwi-like_ProArk	e5xq2B6	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_piwi-like_ProArk	ECOD (1.6)
E [auth B]	Piwi_C_1	e5xq2B5	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	2.170.260.50	Mainly Beta	Beta Complex	paz domain		CATH (utative)
A	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (utative)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
E [auth B]	2.170.260.50	Mainly Beta	Beta Complex	paz domain		CATH (utative)
E [auth B]	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (utative)
E [auth B]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, E [auth B]	PF22472	Argonaute, N-terminal domain (Ago_N_2)	Argonaute, N-terminal domain	This domain is found at the N-terminal end of Protein argonaute from Thermus thermophilus (Ago), a site-specific DNA-guided endoRNase organised into four domain: N (this entry), PAZ (Pfam:PF18309), Mid and PIWI (Pfam:PF02171). This domain shows a mix ...	This domain is found at the N-terminal end of Protein argonaute from Thermus thermophilus (Ago), a site-specific DNA-guided endoRNase organised into four domain: N (this entry), PAZ (Pfam:PF18309), Mid and PIWI (Pfam:PF02171). This domain shows a mixed alpha-beta structure [1].	Domain
A, E [auth B]	PF22474	Argonaute, middle domain (Ago_Mid)	Argonaute, middle domain	This domain is found centrally in Protein argonaute from Thermus thermophilus (Ago), a site-specific DNA-guided endoRNase organised into four domain: N (Pfam:PF22472), PAZ (Pfam:PF18309), Mid (this entry) and PIWI (Pfam:PF02171). This domain contains ...	This domain is found centrally in Protein argonaute from Thermus thermophilus (Ago), a site-specific DNA-guided endoRNase organised into four domain: N (Pfam:PF22472), PAZ (Pfam:PF18309), Mid (this entry) and PIWI (Pfam:PF02171). This domain contains residues that have been reported to be critical for cleavage activity. It folds into an alpha-beta three layered sandwich [1].	Domain
A, E [auth B]	PF18309	Argonaute PAZ domain (PAZ_3)	Argonaute PAZ domain	This is a PAZ domain is found in argonaute present in Thermus thermophiles. Argonaute has a central role in the RNA interference pathway by mediating the maturation of small interfering RNA (siRNA) through initial degradation of the passenger strand ...	This is a PAZ domain is found in argonaute present in Thermus thermophiles. Argonaute has a central role in the RNA interference pathway by mediating the maturation of small interfering RNA (siRNA) through initial degradation of the passenger strand, followed by guide-strand-mediated sequence-specific cleavage of target mRNA. The nucleic-acid-binding channel is thought to be positioned between the PAZ and PIWI domain [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, E [auth B]	TtAgo (D546N)	DNA binding binding nucleic acid 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 cation binding manganese ion binding transition metal ion binding ion binding DNA binding binding nucleic acid 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 cation binding manganese ion binding transition metal ion binding ion binding metal ion binding small molecule binding RNA binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process 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 nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process 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	-
B [auth X], F [auth E]	DNA (5'-D(PTPGPAPAPGPAPTPAPGPTPAPGPGPTPTPGP*T)-3')	-	-	-
C [auth Y], G [auth F]	DNA (5'-D(APCPAPAPCPCPTPAPCPTPAPCPCPTPCPG)-3')	-	-	-
D [auth C], H [auth D]	DNA (5'-D(APGP*T)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, E [auth B]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, E [auth B]	IPR040895	Argonaute, PAZ domain	Domain
A, E [auth B]	IPR054763	Argonaute, middle domain	Domain
A, E [auth B]	IPR003100	PAZ domain	Domain
A, E [auth B]	IPR054764	Argonaute, N-terminal domain, thermus	Domain
A, E [auth B]	IPR003165	Piwi domain	Domain
A, E [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.