5YGF

Crystal structure of Drosophila melanogaster Papi extended Tudor domain (D287A) in complex with Piwi N-terminal R10-unme peptide

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	F_UNCLASSIFIED	e5ygfA2	A: beta barrels	X: OB-fold	H: Staphylococcal nuclease (From Topology)	T: Staphylococcal nuclease	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF00567	e5ygfA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF00567	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.50.90	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
A	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00567	Tudor domain (TUDOR)	Tudor domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	GH18329p	RNA binding binding organic cyclic compound binding nucleic acid 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 primary piRNA processing piRNA processing negative regulation of biological process RNA 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 primary piRNA processing piRNA processing negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process RNA processing negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process nucleic acid metabolic process regulatory ncRNA processing regulatory ncRNA-mediated gene silencing regulation of cellular biosynthetic process regulation of gene expression organic cyclic compound metabolic process negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process retrotransposon silencing transposition retrotransposition multicellular organismal process blastoderm segmentation cellular developmental process anterior/posterior pattern specification anterior/posterior axis specification, embryo segmentation pattern specification process cell development cellular process involved in reproduction in multicellular organism female gamete generation embryo development oocyte development tripartite regional subdivision cellular component organization cellular component biogenesis embryonic axis specification multicellular organism development cellular component assembly anterior/posterior axis specification cell differentiation anatomical structure development cellular component organization or biogenesis cell maturation P granule organization embryonic pattern specification oocyte axis specification oocyte construction oogenesis oocyte anterior/posterior axis specification developmental maturation cytoplasm organization regionalization organelle organization pole plasm assembly anatomical structure maturation maternal determination of anterior/posterior axis, embryo germ cell development oocyte differentiation axis specification	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle P granule cytoplasmic ribonucleoprotein granule germ plasm ribonucleoprotein granule pole plasm intracellular non-membrane-bounded organelle membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle P granule cytoplasmic ribonucleoprotein granule germ plasm ribonucleoprotein granule pole plasm intracellular non-membrane-bounded organelle supramolecular complex non-membrane-bounded organelle P-body protein-containing complex nucleus
B [auth D]	ASP-GLN-GLY-ARG-GLY-ARG-ARG-ARG-PRO	RNA binding binding organic cyclic compound binding nucleic acid binding DNA binding protein-containing complex binding chromatin binding chromatin DNA binding regulatory RNA binding piRNA binding endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA RNA binding binding organic cyclic compound binding nucleic acid binding DNA binding protein-containing complex binding chromatin binding chromatin DNA 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 cellular developmental process oogenesis cell development cellular process involved in reproduction in multicellular organism female gamete generation cell differentiation developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation cellular developmental process oogenesis cell development cellular process involved in reproduction in multicellular organism female gamete generation cell differentiation anatomical structure development germ cell development cellular process regulation of biological process regulation of cellular process negative regulation of cellular process biological regulation negative regulation of biological process retrotransposon silencing transposition retrotransposition multicellular organismal process germ-line stem cell population maintenance maintenance of cell number stem cell population maintenance cellular biosynthetic process negative regulation of cellular metabolic process post-transcriptional regulation of gene expression organic substance metabolic process organic substance biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process protein-DNA complex organization cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis heterochromatin formation protein-containing complex organization epigenetic regulation of gene expression regulatory ncRNA-mediated gene silencing regulatory ncRNA-mediated heterochromatin formation piRNA-mediated heterochromatin formation negative regulation of gene expression, epigenetic positive regulation of nuclear-transcribed mRNA poly(A) tail shortening regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of mRNA metabolic process primary metabolic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process nuclear-transcribed mRNA poly(A) tail shortening organic cyclic compound metabolic process nucleic acid catabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process positive regulation of biological process RNA metabolic process macromolecule catabolic process mRNA destabilization regulation of mRNA catabolic process regulation of nuclear-transcribed mRNA poly(A) tail shortening nuclear-transcribed mRNA catabolic process RNA destabilization regulation of catabolic process mRNA metabolic process nucleic acid metabolic process organic cyclic compound catabolic process positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process organic substance catabolic process retrotransposon silencing by heterochromatin formation piRNA-mediated retrotransposon silencing by heterochromatin formation stem cell division asymmetric cell division germ-line stem cell division male germ-line stem cell asymmetric division cell division asymmetric stem cell division germline stem cell asymmetric division primary piRNA processing piRNA processing RNA processing regulatory ncRNA processing positive regulation of organelle organization cellular component biogenesis regulation of heterochromatin formation regulation of chromatin organization regulation of DNA methylation-dependent heterochromatin formation regulation of chromosome organization regulation of organelle organization positive regulation of chromosome organization regulation of cellular component organization positive regulation of cellular component organization positive regulation of DNA methylation-dependent heterochromatin formation positive regulation of heterochromatin formation DNA methylation-dependent heterochromatin formation positive regulation of chromatin organization positive regulation of cellular process positive regulation of cellular component biogenesis chromosome organization regulation of cellular component biogenesis organelle organization facultative heterochromatin formation cell fate determination germarium-derived oocyte fate determination oocyte fate determination germarium-derived egg chamber formation germarium-derived oocyte differentiation anatomical structure morphogenesis anatomical structure formation involved in morphogenesis oocyte differentiation cell fate commitment cellularization pole cell formation multicellular organism development pole cell development female germ-line stem cell asymmetric division	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle P granule cytoplasmic ribonucleoprotein granule germ plasm ribonucleoprotein granule pole plasm intracellular non-membrane-bounded organelle membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle P granule cytoplasmic ribonucleoprotein granule germ plasm ribonucleoprotein granule pole plasm intracellular non-membrane-bounded organelle supramolecular complex non-membrane-bounded organelle nucleus germ cell nucleus cytosol membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex protein-DNA complex chromatin chromosome Yb body heterochromatin chromocenter euchromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002999	Tudor domain	Domain
A	IPR035437	SNase-like, OB-fold superfamily	Homologous Superfamily
A	IPR004087	K Homology domain	Domain
A	IPR036612	K Homology domain, type 1 superfamily	Homologous Superfamily
A	IPR047380	Tudor domain-containing protein 2-like, tudor domain	Domain
A	IPR004088	K Homology domain, type 1	Domain
B [auth D]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
B [auth D]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
B [auth D]	IPR003100	PAZ domain	Domain
B [auth D]	IPR036085	PAZ domain superfamily	Homologous Superfamily
B [auth D]	IPR003165	Piwi domain	Domain

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 R01GM133198.