4B9W

Structure of extended Tudor domain TD3 from mouse TDRD1 in complex with MILI peptide containing dimethylarginine 45.

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	SN_TDRD1	e4b9wA1	A: beta barrels	X: OB-fold	H: Staphylococcal nuclease (From Topology)	T: Staphylococcal nuclease	F: SN_TDRD1	ECOD (1.6)
A	TUDOR	e4b9wA2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: TUDOR	ECOD (1.6)
B	SN_TDRD1	e4b9wB1	A: beta barrels	X: OB-fold	H: Staphylococcal nuclease (From Topology)	T: Staphylococcal nuclease	F: SN_TDRD1	ECOD (1.6)
B	TUDOR	e4b9wB2	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)
B	2.40.50.90	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
B	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, B	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, B	TUDOR DOMAIN-CONTAINING PROTEIN 1	cation binding ion binding 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 cell development cellular process involved in reproduction in multicellular organism cell differentiation anatomical structure development germ cell development developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation cellular developmental process cell development cellular process involved in reproduction in multicellular organism cell differentiation anatomical structure development germ cell development cellular process regulation of cellular process cellular biosynthetic process negative regulation of biological process retrotransposon silencing negative regulation of cellular metabolic process cellular component organization retrotransposon silencing by piRNA-directed DNA methylation chromatin organization negative regulation of cellular process DNA methylation-dependent heterochromatin formation chromatin remodeling retrotransposon silencing by heterochromatin formation cellular component organization or biogenesis retrotransposition negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process transposition gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation biosynthetic process regulatory ncRNA-mediated heterochromatin formation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process gene silencing by piRNA-directed DNA methylation piRNA-mediated heterochromatin formation macromolecule metabolic process regulation of metabolic process 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 meiotic cell cycle cell cycle multicellular organismal process blastoderm segmentation anterior/posterior pattern specification anterior/posterior axis specification, embryo segmentation pattern specification process female gamete generation embryo development oocyte development tripartite regional subdivision cellular component biogenesis embryonic axis specification multicellular organism development cellular component assembly anterior/posterior axis specification 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 oocyte differentiation axis specification	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 pi-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 pi-body synapse cell junction cytosol protein-containing complex ribonucleoprotein complex chromatoid body
C [auth P], D [auth S]	PIWI-LIKE PROTEIN 2	RNA binding binding organic cyclic compound binding nucleic acid binding mRNA 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 RNA binding binding organic cyclic compound binding nucleic acid binding mRNA 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 cellular process negative regulation of biological process negative regulation of cellular metabolic process 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 regulation of biological process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process negative regulation of metabolic process positive regulation of mRNA metabolic process regulation of cellular metabolic process primary metabolic process negative regulation of cellular biosynthetic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process catabolic process cellular biosynthetic process positive regulation of biological process RNA metabolic process mRNA destabilization macromolecule catabolic process regulation of mRNA catabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process RNA destabilization biological regulation regulation of macromolecule metabolic process regulation of catabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process regulatory ncRNA-mediated post-transcriptional gene silencing regulation of cellular biosynthetic process positive regulation of catabolic process regulation of mRNA stability regulatory ncRNA-mediated gene silencing negative regulation of biosynthetic process 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 piRNA processing RNA biosynthetic process nucleic acid biosynthetic process RNA processing secondary piRNA processing nucleobase-containing compound biosynthetic process regulatory ncRNA processing rhythmic process circadian rhythm negative regulation of circadian rhythm regulation of circadian rhythm retrotransposon silencing cellular component organization chromatin organization chromatin remodeling retrotransposon silencing by heterochromatin formation cellular component organization or biogenesis retrotransposition heterochromatin formation epigenetic regulation of gene expression piRNA-mediated retrotransposon silencing by heterochromatin formation transposition regulatory ncRNA-mediated heterochromatin formation piRNA-mediated heterochromatin formation negative regulation of gene expression, epigenetic positive regulation of protein metabolic process positive regulation of translation positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of cytoplasmic translation positive regulation of biosynthetic process protein metabolic process positive regulation of cellular process regulation of protein metabolic process translation positive regulation of gene expression regulation of translation cytoplasmic translation regulation of cytoplasmic translation positive regulation of cellular biosynthetic process retrotransposon silencing by piRNA-directed DNA methylation DNA methylation-dependent heterochromatin formation constitutive heterochromatin formation gene silencing by piRNA-directed DNA methylation positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization regulation of reproductive process meiotic cell cycle process regulation of meiosis I meiosis I positive regulation of cell cycle process meiotic nuclear division cell cycle regulation of cell cycle cell cycle process positive regulation of reproductive process regulation of meiotic cell cycle regulation of cell cycle process organelle fission meiotic cell cycle positive regulation of nuclear division positive regulation of meiotic cell cycle regulation of organelle organization positive regulation of cell cycle regulation of meiotic nuclear division organelle organization nuclear division meiosis I cell cycle process positive regulation of meiosis I regulation of nuclear division positive regulation of meiotic nuclear division retrotransposon silencing by mRNA destabilization	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 cytosol 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 cytosol dense body chromatoid body pi-body perinucleolar chromocenter chromocenter protein-containing complex PET complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR002893	Zinc finger, MYND-type	Domain
A, B	IPR047378	Tudor domain-containing protein 1, third Tudor domain	Domain
A, B	IPR002999	Tudor domain	Domain
A, B	IPR047376	Tudor domain-containing protein 1, first Tudor domain	Domain
A, B	IPR035437	SNase-like, OB-fold superfamily	Homologous Superfamily
A, B	IPR047377	Tudor domain-containing protein 1, second Tudor domain	Domain
A, B	IPR050621	Tudor domain-containing	Family
C [auth P], D [auth S]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
C [auth P], D [auth S]	IPR014811	Argonaute, linker 1 domain	Domain
C [auth P], D [auth S]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
C [auth P], D [auth S]	IPR003100	PAZ domain	Domain
C [auth P], D [auth S]	IPR036085	PAZ domain superfamily	Homologous Superfamily
C [auth P], D [auth S]	IPR003165	Piwi domain	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C [auth P], D [auth S]	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.