5YGD | pdb_00005ygd

Crystal structure of Drosophila melanogaster Papi extended Tudor domain (D287A) in complex with Piwi N-terminal R10me2s peptide

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	KOG2279	e5ygdA1	A: beta barrels	X: OB-fold	H: Staphylococcal nuclease (From Topology)	T: Staphylococcal nuclease	F: KOG2279	ECOD (1.6)
A	TUDOR	e5ygdA2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: TUDOR	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
B [auth D]	ASP-GLN-GLY-ARG-GLY-ARG-2MR-ARG-PRO-LEU-ASN	RNA binding binding nucleic acid binding DNA binding chromatin binding chromatin DNA binding regulatory RNA binding piRNA binding endonuclease activity nuclease activity catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity RNA binding binding nucleic acid binding DNA binding chromatin binding chromatin DNA binding regulatory RNA binding piRNA binding endonuclease activity nuclease activity catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity cation binding ion binding metal ion binding small molecule binding	regulation of cellular process negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process retrotransposition regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression transposition macromolecule biosynthetic process regulation of gene expression regulation of cellular process negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process retrotransposition regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression transposition macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process transposable element silencing regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process 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 regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression 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 mRNA metabolic process primary metabolic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process post-transcriptional gene silencing nucleic acid catabolic process catabolic process positive regulation of biological process RNA metabolic process mRNA destabilization macromolecule catabolic process regulation of mRNA catabolic process positive regulation of cellular process RNA destabilization regulation of catabolic process mRNA metabolic process nucleic acid metabolic process regulatory ncRNA-mediated post-transcriptional gene silencing positive regulation of catabolic process regulation of mRNA stability regulatory ncRNA-mediated gene silencing positive regulation of mRNA catabolic process regulation of RNA stability piRNA-mediated gene silencing by mRNA destabilization regulation of mRNA metabolic process multicellular organismal process germ-line stem cell population maintenance maintenance of cell number stem cell population maintenance cellular component organization cellular component biogenesis cellular component assembly chromatin organization chromatin remodeling cellular component organization or biogenesis heterochromatin formation epigenetic regulation of gene expression transposable element silencing by piRNA-mediated heterochromatin formation transposable element silencing by heterochromatin formation heterochromatin organization constitutive heterochromatin formation regulatory ncRNA-mediated heterochromatin formation piRNA-mediated heterochromatin formation negative regulation of gene expression, epigenetic 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 biosynthetic process nucleic acid biosynthetic process RNA processing nucleobase-containing compound biosynthetic process regulatory ncRNA processing 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	intracellular anatomical structure P granule cytoplasmic ribonucleoprotein granule germ plasm intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle pole plasm membraneless organelle cytoplasm supramolecular complex membrane-bounded organelle intracellular anatomical structure P granule cytoplasmic ribonucleoprotein granule germ plasm intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle pole plasm membraneless organelle cytoplasm supramolecular complex membrane-bounded organelle nucleus germ cell nucleus intracellular membrane-bounded organelle cytosol membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen chromatin chromosome protein-containing complex RNA polymerase II transcription repressor complex nuclear protein-containing complex transcription regulator complex transcription repressor complex Yb body heterochromatin chromocenter euchromatin
A	GH18329p	RNA binding binding nucleic acid binding	regulation of cellular process negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process retrotransposition regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression transposition macromolecule biosynthetic process regulation of gene expression regulation of cellular process negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process retrotransposition regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression transposition macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process transposable element silencing regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation primary piRNA processing piRNA processing RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process RNA processing primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulatory ncRNA processing regulatory ncRNA-mediated gene silencing multicellular organismal process blastoderm segmentation cellular developmental process anterior/posterior pattern specification anterior/posterior axis specification, embryo segmentation cell development cellular process involved in reproduction in multicellular organism pattern specification process 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 cytoplasm organization developmental maturation 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 cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle P granule cytoplasmic ribonucleoprotein granule germ plasm intracellular membraneless organelle ribonucleoprotein granule pole plasm membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle P granule cytoplasmic ribonucleoprotein granule germ plasm intracellular membraneless organelle ribonucleoprotein granule pole plasm membraneless organelle supramolecular complex protein-containing complex nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
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	IPR050621	Tudor domain-containing	Family
A	IPR004088	K Homology domain, type 1	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth D]	2MR	Parent Component: ARG RESID: AA0067 PSI-MOD : symmetric dimethyl-L-arginine MOD:00076

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.