5M9N | pdb_00005m9n

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)
B	MMS1_N	e5m9nB1	A: alpha bundles	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (develop294)
A	TUDOR	e5m9nA2	A: alpha bundles	X: SH3	H: SH3	T: SH3	F: TUDOR	ECOD (develop294)

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
C	E2F peptide	sequence-specific DNA binding DNA binding binding nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding molecular adaptor activity protein binding sequence-specific DNA binding DNA binding binding nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding molecular adaptor activity protein binding protein dimerization activity RNA polymerase II transcription regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding DNA-binding transcription activator activity kinase binding enzyme binding protein kinase binding transcription factor binding DNA-binding transcription factor binding	developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation signal transduction by p53 class mediator cell death intracellular signal transduction cell communication apoptotic signaling pathway intrinsic apoptotic signaling pathway by p53 class mediator cellular process signal transduction apoptotic process intrinsic apoptotic signaling pathway programmed cell death regulation of biosynthetic process positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process response to decreased oxygen levels cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to chemical response to oxygen levels response to abiotic stimulus 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 RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to nerve growth factor stimulus response to nerve growth factor response to growth factor regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of DNA-templated transcription quinolinate metabolic process oxoacid metabolic process small molecule biosynthetic process dicarboxylic acid metabolic process pyridine-containing compound biosynthetic process carboxylic acid metabolic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process quinolinate biosynthetic process pyridine-containing compound metabolic process small molecule metabolic process dicarboxylic acid biosynthetic process cellular response to xenobiotic stimulus response to xenobiotic stimulus negative regulation of biological process negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process anoikis positive regulation of DNA-templated transcription positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process DNA damage checkpoint signaling regulation of cell cycle phase transition negative regulation of cell cycle cell cycle phase transition negative regulation of cell cycle phase transition cell cycle regulation of cell cycle cell cycle process regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling DNA damage response signal transduction in response to DNA damage 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 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 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 intrinsic apoptotic signaling pathway in response to DNA damage 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 response to lipid response to fatty acid response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to fatty acid cellular response to lipid positive regulation of nervous system development cell development regulation of neurogenesis regulation of gliogenesis positive regulation of glial cell proliferation positive regulation of gliogenesis regulation of cell development regulation of nervous system development positive regulation of developmental process neurogenesis regulation of glial cell proliferation gliogenesis positive regulation of cell differentiation regulation of multicellular organismal process positive regulation of neurogenesis regulation of multicellular organismal development positive regulation of cell development positive regulation of multicellular organismal process glial cell proliferation 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 G1/S transition of mitotic cell cycle mitotic cell cycle phase transition biological process involved in interspecies interaction between organisms response to other organism response to external stimulus response to lipopolysaccharide response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin	cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus membrane-enclosed lumen nuclear chromosome intracellular membrane-bounded organelle cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus membrane-enclosed lumen nuclear chromosome intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen nuclear lumen RNA polymerase II transcription regulator complex protein-containing complex nuclear protein-containing complex transcription regulator complex centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton nucleoplasm Rb-E2F complex
A, B	Tudor domain-containing protein 1	cation binding transition metal ion binding zinc ion 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 piRNA processing negative regulation of biological process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process negative regulation of cellular process RNA processing negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process regulatory ncRNA processing regulatory ncRNA-mediated gene silencing regulation of gene expression 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 macromolecule metabolic process regulation of metabolic process meiotic cell cycle cell cycle cellular component organization cellular component biogenesis cellular component assembly chromatin organization chromatin remodeling cellular component organization or biogenesis retrotransposition heterochromatin formation epigenetic regulation of gene expression transposable element silencing by heterochromatin formation heterochromatin organization transposition constitutive heterochromatin formation regulatory ncRNA-mediated heterochromatin formation transposable element silencing by piRNA-mediated DNA methylation DNA methylation-dependent constitutive heterochromatin formation transposable element silencing negative regulation of gene expression, epigenetic gene silencing by piRNA-directed DNA methylation piRNA-mediated heterochromatin formation 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 embryonic axis specification multicellular organism development anterior/posterior axis specification 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 oocyte differentiation axis specification	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 pi-body 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 pi-body synapse cell junction protein-containing complex ribonucleoprotein complex chromatoid body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
C	IPR032198	E2F transcription factor, CC-MB domain	Domain
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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
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
A, B	Pharos: Q9BXT4	large cell medulloblastoma malignant colon neoplasm

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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