4F1N | pdb_00004f1n

Crystal structure of Kluyveromyces polysporus Argonaute with a 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)
A	SCOP2 Family	N-terminal domain of argonaute	8053662	4004602	SCOP2 (2022-06-29)
A	SCOP2 Family	PAZ domain	8053663	4000853	SCOP2 (2022-06-29)
A	SCOP2 Family	Mid domain of argonaute	8053664	4004605	SCOP2 (2022-06-29)
A	SCOP2 Family	PIWI domain	8053665	4002242	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RNA-binding domain, RBD	8053671	3000110	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PAZ domain	8053672	3001750	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Mid domain of argonaute	8053673	3002210	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribonuclease H-like	8053674	3000143	SCOP2 (2022-06-29)
C [auth B]	SCOP2B Superfamily	Ribonuclease H-like	8053674	3000143	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Mid domain of argonaute	8053673	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)
A	PAZ_1	e4f1nA3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PAZ_1	ECOD (1.6)
A	ArgoL1	e4f1nA2	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: ArgoL1	ECOD (1.6)
A	EUF08365	e4f1nA1	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: EUF08365	ECOD (1.6)
A	Piwi_N_1	e4f1nA4	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_1	ECOD (1.6)
A	Piwi_C	e4f1nA5	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Piwi_C	ECOD (1.6)
C [auth B]	PAZ_1	e4f1nB6	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PAZ_1	ECOD (1.6)
C [auth B]	ArgoL1	e4f1nB5	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: ArgoL1	ECOD (1.6)
C [auth B]	EUF08365	e4f1nB4	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: EUF08365	ECOD (1.6)
C [auth B]	Piwi_N_1	e4f1nB3	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_1	ECOD (1.6)
C [auth B]	Piwi_C	e4f1nB2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Piwi_C	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B]	PF18351	Fungal Argonaute N-terminal domain (Ago_N_1)	Fungal Argonaute N-terminal domain	The AGO (Argonaute) proteins have four domains: an N-terminal domain, the PAZ domain, the MID domain and the PIWI domain. This entry is for the N-terminal domain. The N-terminal domain of AGOs is the most variable domain. Compared with prokaryotic Ar ...	The AGO (Argonaute) proteins have four domains: an N-terminal domain, the PAZ domain, the MID domain and the PIWI domain. This entry is for the N-terminal domain. The N-terminal domain of AGOs is the most variable domain. Compared with prokaryotic Argonautes, KpAGO (Kluyveromyces polysporus Argonaute) has numerous surface-exposed insertion segments, with a cluster of conserved insertions re-positioning the N domain, contributing to the formation of nucleic-acid-binding channel to enable full propagation of the 3' end of the guide RNA guide-target pairing. The guide strand is used by the RISC complex to specify interactions with target RNAs. If sequence complementarity between guide and target is extensive, AGO catalyses cleavage, resulting in slicing of the target RNA [1].	Domain
A, C [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
A, C [auth B]	PF02170	PAZ domain (PAZ)	PAZ domain	This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel ...	This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerisation. The three-dimensional structure of this domain has been solved [2-4]. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteristic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway.	Domain
A, C [auth B]	PF18236	Argonaute N domain (AGO_N)	Argonaute N domain	This is the N domain often found in the N-terminal region of Argonaute (AGO) present in Kluyveromyces polyspora. AGO forms part of the RNA-induced silencing complex that mediates the gene silencing pathway, RNA interference. The N domain blocks the n ...	This is the N domain often found in the N-terminal region of Argonaute (AGO) present in Kluyveromyces polyspora. AGO forms part of the RNA-induced silencing complex that mediates the gene silencing pathway, RNA interference. The N domain blocks the nucleic acid-binding channel and prevents propagation of guide-target pairing beyond position 16 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth E], D [auth F]	RNA 5'-R(PUPAPAPAPAPAPAPAP*A)-3'	-	-	-
A, C [auth B]	KpAGO	RNA binding binding nucleic acid binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B]	IPR040937	Argonaute, N-terminal	Domain
A, C [auth B]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, C [auth B]	IPR036085	PAZ domain superfamily	Homologous Superfamily
A, C [auth B]	IPR040588	Argonaute, N domain	Domain
A, C [auth B]	IPR003165	Piwi domain	Domain
A, C [auth B]	IPR003100	PAZ domain	Domain
A, C [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.