3O6E

Crystal Structure of human Hiwi1 PAZ domain (residues 277-399) in complex with 14-mer RNA (12-bp + 2-nt overhang) containing 2'-OCH3 at its 3'-end

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth X]	SCOP2B Superfamily	PAZ domain	8100398	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 [auth X]	PAZ	e3o6eX1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PAZ	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth X]	2.170.260.10	Mainly Beta	Beta Complex	paz domain	paz domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth X]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth X]	Piwi-like protein 1	mRNA cap binding complex binding protein-containing complex binding binding RNA binding organic cyclic compound binding nucleic acid binding single-stranded RNA binding mRNA binding protein binding kinase binding enzyme binding protein kinase binding regulatory RNA binding piRNA binding mRNA cap binding complex binding protein-containing complex binding binding RNA binding organic cyclic compound binding nucleic acid binding single-stranded RNA binding mRNA binding protein binding kinase binding enzyme binding protein kinase binding regulatory RNA binding piRNA 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 cation binding ion binding metal ion binding small molecule binding	developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation regulation of cellular process cellular biosynthetic process organonitrogen compound biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression organic substance metabolic process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation regulation of cellular process cellular biosynthetic process organonitrogen compound biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression organic substance metabolic process organic substance biosynthetic process protein metabolic process regulation of biosynthetic process regulation of biological process organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of translation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process negative regulation of biological process retrotransposon silencing negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling retrotransposon silencing by heterochromatin formation cellular component organization or biogenesis negative regulation of macromolecule metabolic process retrotransposition heterochromatin formation protein-containing complex organization epigenetic regulation of gene expression negative regulation of metabolic process piRNA-mediated retrotransposon silencing by heterochromatin formation transposition negative regulation of cellular biosynthetic process regulatory ncRNA-mediated gene silencing negative regulation of gene expression regulatory ncRNA-mediated heterochromatin formation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process piRNA-mediated heterochromatin formation negative regulation of gene expression, epigenetic spermatid development spermatid differentiation cellular developmental process cell development cellular process involved in reproduction in multicellular organism cell differentiation anatomical structure development germ cell development sperm DNA condensation nucleus organization organelle organization spermatid nucleus differentiation primary piRNA processing piRNA processing RNA metabolic process nucleobase-containing compound metabolic process RNA processing nucleic acid metabolic process regulatory ncRNA processing organic cyclic compound metabolic process meiotic cell cycle cell cycle	intracellular anatomical structure P granule cytoplasmic ribonucleoprotein granule germ plasm cellular anatomical entity ribonucleoprotein granule intracellular organelle organelle pole plasm intracellular non-membrane-bounded organelle cytoplasm supramolecular complex non-membrane-bounded organelle dense body intracellular anatomical structure P granule cytoplasmic ribonucleoprotein granule germ plasm cellular anatomical entity ribonucleoprotein granule intracellular organelle organelle pole plasm intracellular non-membrane-bounded organelle cytoplasm supramolecular complex non-membrane-bounded organelle dense body chromatoid body membrane-bounded organelle nucleus intracellular membrane-bounded organelle
B [auth A]	RNA (5'-R(GPCPGPAPAPUPAPUPUPCPGPCPUP(OMU))-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth X]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A [auth X]	IPR014811	Argonaute, linker 1 domain	Domain
A [auth X]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A [auth X]	IPR031320	GAGE	Domain
A [auth X]	IPR003100	PAZ domain	Domain
A [auth X]	IPR036085	PAZ domain superfamily	Homologous Superfamily
A [auth X]	IPR003165	Piwi domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth X]	Pharos: Q96J94	Drug abuse substance dependence drug dependence malignant colon neoplasm substance abuse substance-related disorder

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.