5M9N

Crystal structure of human TDRD1 extended Tudor domain in complex with a symmetrically dimethylated E2F peptide

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
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	e5m9nA1	A: beta barrels	X: OB-fold	H: Staphylococcal nuclease (From Topology)	T: Staphylococcal nuclease	F: SN_TDRD1	ECOD (1.6)
A	TUDOR	e5m9nA2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: TUDOR	ECOD (1.6)
B	SN_TDRD1	e5m9nB1	A: beta barrels	X: OB-fold	H: Staphylococcal nuclease (From Topology)	T: Staphylococcal nuclease	F: SN_TDRD1	ECOD (1.6)
B	TUDOR	e5m9nB2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: TUDOR	ECOD (1.6)

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 siRNA-mediated heterochromatin formation siRNA-mediated retrotransposon silencing by heterochromatin formation 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 protein-containing complex ribonucleoprotein complex chromatoid body
C	E2F peptide	DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription regulator activity DNA-binding transcription factor activity DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity DNA-binding transcription factor activity, RNA polymerase II-specific transcription factor binding protein binding DNA-binding transcription factor binding molecular adaptor activity protein dimerization activity	regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process developmental process fat cell differentiation regulation of developmental process cellular developmental process negative regulation of developmental process regulation of cell differentiation negative regulation of fat cell differentiation cell differentiation negative regulation of cell differentiation regulation of fat cell differentiation cellular response to stimulus response to stimulus signaling signal transduction by p53 class mediator cell death intracellular signal transduction cell communication apoptotic signaling pathway intrinsic apoptotic signaling pathway by p53 class mediator signal transduction apoptotic process intrinsic apoptotic signaling pathway programmed cell death positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of gene expression positive regulation of cellular biosynthetic process fibroblast proliferation cell population proliferation positive regulation of cell population proliferation regulation of fibroblast proliferation regulation of cell population proliferation positive regulation of fibroblast proliferation positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death positive regulation of apoptotic process epithelial cell apoptotic process lens fiber cell apoptotic process post-transcriptional regulation of gene expression regulation of biological quality RNA catabolic process mRNA stabilization mRNA catabolic process nucleobase-containing compound catabolic process negative regulation of gene expression nucleic acid catabolic process catabolic process macromolecule catabolic process negative regulation of mRNA metabolic process regulation of mRNA catabolic process negative regulation of catabolic process negative regulation of mRNA catabolic process negative regulation of RNA catabolic process regulation of catabolic process mRNA metabolic process regulation of mRNA stability RNA stabilization regulation of RNA stability regulation of mRNA metabolic process negative regulation of cell population proliferation fat cell proliferation regulation of fat cell proliferation negative regulation of fat cell proliferation multicellular organismal process head development forebrain development animal organ development brain development nervous system development multicellular organism development central nervous system development anatomical structure development system development cellular response to stress DNA damage response response to stress intrinsic apoptotic signaling pathway in response to DNA damage positive regulation of DNA-templated transcription positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process cellular response to chemical stimulus response to chemical cellular response to xenobiotic stimulus response to xenobiotic stimulus regulation of molecular function regulation of DNA binding regulation of binding negative regulation of binding negative regulation of molecular function negative regulation of DNA binding transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II regulation of cell cycle phase transition regulation of cell cycle process cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition mitotic cell cycle regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle regulation of G1/S transition of mitotic cell cycle mitotic cell cycle process cell cycle regulation of cell cycle G1/S transition of mitotic cell cycle cell cycle process mitotic cell cycle phase transition anoikis positive regulation of transcription by RNA polymerase II DNA damage checkpoint signaling negative regulation of cell cycle negative regulation of cell cycle phase transition DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling signal transduction in response to DNA damage	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle centrosome microtubule organizing center cytoskeleton RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle centrosome microtubule organizing center cytoskeleton intracellular non-membrane-bounded organelle microtubule cytoskeleton non-membrane-bounded organelle cytoplasm membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen chromatin chromosome Rb-E2F complex

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	IPR032198	E2F transcription factor, CC-MB domain	Domain
C	IPR037241	E2F-DP heterodimerization region	Homologous Superfamily
C	IPR003316	E2F/DP family, winged-helix DNA-binding domain	Domain
C	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
C	IPR015633	E2F Family	Family
C	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9BXT4	large cell medulloblastoma malignant colon neoplasm
C	Pharos: Q01094	melanoma breast cancer breast carcinoma cutaneous melanoma hepatocellular carcinoma malignant mesothelioma Mammary Neoplasms, Human skin carcinoma eye disease large cell medulloblastoma cancer glioblastoma ovarian cancer

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C	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.