5I4A | pdb_00005i4a

X-ray crystal structure of Marinitoga piezophila Argonaute in complex with 5' OH guide RNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
C	SCOP2 Family	N-terminal domain of argonaute	8053677	4004602	SCOP2 (2022-06-29)
C	SCOP2 Family	PAZ domain	8053678	4000853	SCOP2 (2022-06-29)
C	SCOP2 Family	Mid domain of argonaute	8053679	4004605	SCOP2 (2022-06-29)
C	SCOP2 Family	PIWI domain	8053680	4002242	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	RNA-binding domain, RBD	8053683	3000110	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	PAZ domain	8053684	3001750	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Mid domain of argonaute	8053685	3002210	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Ribonuclease H-like	8053686	3000143	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8053686	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Mid domain of argonaute	8053685	3002210	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RNA-binding domain, RBD	8053683	3000110	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PAZ domain	8053684	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)
C	EUF07580	e5i4aC4	A: beta barrels	X: SH3	H: SH3	T: SH3	F: EUF07580	ECOD (1.6)
C	EUF08371	e5i4aC3	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: EUF08371	ECOD (1.6)
C	EUF08372	e5i4aC1	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: EUF08372	ECOD (1.6)
C	EUF08635	e5i4aC2	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: EUF08635	ECOD (1.6)
C	Piwi_C_1	e5i4aC5	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)
A	EUF07580	e5i4aA3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: EUF07580	ECOD (1.6)
A	EUF08371	e5i4aA1	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: EUF08371	ECOD (1.6)
A	EUF08372	e5i4aA2	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: EUF08372	ECOD (1.6)
A	EUF08635	e5i4aA4	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: EUF08635	ECOD (1.6)
A	Piwi_C_1	e5i4aA5	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF22136	Bacterial argonaute protein N-terminal domain (MpAgo_N-like)	Bacterial argonaute protein N-terminal domain	Argonaute proteins are key effectors of eukaryotic RNA interference and, in prokaryotes, function in host genome defense. This entry represents a domain found at the N-terminus of the Marinitoga piezophila Argonaute (MpAgo) protein that uses 5'-hydr ...	Argonaute proteins are key effectors of eukaryotic RNA interference and, in prokaryotes, function in host genome defense. This entry represents a domain found at the N-terminus of the Marinitoga piezophila Argonaute (MpAgo) protein that uses 5'-hydroxylated guide RNAs to recognise and cleave single-stranded target sequences rather than the 5'-phosphorylated guides used by all known Argonautes [1]. This domain adopts alpha/beta structure consisting of four-stranded beta-sheet and two helices. Compared to other Argonaute proteins, this domain differs in both its secondary structure and its orientation relative to the MID/PIWI lobe.	Domain
A, C	PF22362	Argonaute, middle domain, bacteria (Ago_MID_bact)	Argonaute, middle domain, bacteria	This entry represents the middle domain of bacterial argonaute (Ago) [1,2]. Ago bind small RNA or DNA guides which provide base-pairing specificity for recognition and cleavage of complementary nucleic acid targets. Bacterial Ago adopt a bilobed stru ...	This entry represents the middle domain of bacterial argonaute (Ago) [1,2]. Ago bind small RNA or DNA guides which provide base-pairing specificity for recognition and cleavage of complementary nucleic acid targets. Bacterial Ago adopt a bilobed structure; an N-terminal and a PAZ domain constitute one lobe, the second one consists of a middle (MID) domain and the catalytic PIWI domain. This domain mediates the recognition of the 5' end of the guide [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	RNA (5'-R(UPAPUPAPCPAPAPCPCPUPAPCPUPU)-3')	-	-	-
A, C	Argonaute protein	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 RNA binding cation binding ion binding metal 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 RNA binding cation binding ion binding metal ion binding small molecule binding	-	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, C	IPR054387	Argonaute, N-terminal domain, bacteria	Domain
A, C	IPR054434	Argonaute, middle domain, bacteria	Domain
A, C	IPR003165	Piwi domain	Domain
A, C	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.