5M9O | pdb_00005m9o

Crystal structure of human SND1 extended Tudor domain in complex with a symmetrically dimethylated E2F peptide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8042395	3000404	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	SNase_1	e5m9oA1	A: beta barrels	X: OB-fold	H: Staphylococcal nuclease (From Topology)	T: Staphylococcal nuclease	F: SNase_1	ECOD (1.6)
A	TUDOR	e5m9oA2	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	PF00565	Staphylococcal nuclease homologue (SNase)	Staphylococcal nuclease homologue	Present in all three domains of cellular life. Four copies in the transcriptional coactivator p100: these, however, appear to lack the active site residues of Staphylococcal nuclease. Positions 14 (Asp-21), 34 (Arg-35), 39 (Asp-40), 42 (Glu-43) and 1 ...	Present in all three domains of cellular life. Four copies in the transcriptional coactivator p100: these, however, appear to lack the active site residues of Staphylococcal nuclease. Positions 14 (Asp-21), 34 (Arg-35), 39 (Asp-40), 42 (Glu-43) and 110 (Arg-87) [SNase numbering in parentheses] are thought to be involved in substrate-binding and catalysis.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	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 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	Staphylococcal nuclease domain-containing protein 1	nuclease activity catalytic activity, acting on a nucleic acid catalytic activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity RNA binding binding nucleic acid binding RISC complex binding ribonucleoprotein complex binding protein-containing complex binding cell adhesion molecule binding nuclease activity catalytic activity, acting on a nucleic acid catalytic activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity RNA binding binding nucleic acid binding RISC complex binding ribonucleoprotein complex binding protein-containing complex binding cell adhesion molecule binding cadherin binding protein binding endonuclease activity catalytic activity, acting on RNA RNA endonuclease activity RNA nuclease activity	developmental process multicellular organismal process cellular developmental process ossification cell differentiation cellular process osteoblast differentiation regulation of biological process regulation of cellular process regulation of cell cycle process biological regulation cell cycle regulation of cell cycle cell cycle process developmental process multicellular organismal process cellular developmental process ossification cell differentiation cellular process osteoblast differentiation regulation of biological process regulation of cellular process regulation of cell cycle process biological regulation cell cycle regulation of cell cycle cell cycle process catabolic process RNA metabolic process primary metabolic process miRNA catabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process macromolecule metabolic process miRNA metabolic process RNA catabolic process regulation of biosynthetic process negative regulation of metabolic process negative regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process 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 negative regulation of cellular process regulation of macromolecule biosynthetic process regulation of metabolic process negative regulation of macromolecule metabolic process mRNA catabolic process mRNA metabolic process	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle extracellular exosome cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol dense body protein-containing complex ribonucleoprotein complex RNAi effector complex nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR037241	E2F-DP heterodimerization region	Homologous Superfamily
B	IPR003316	E2F/DP family, winged-helix DNA-binding domain	Domain
B	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
B	IPR015633	E2F Family	Family
B	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
B	IPR032198	E2F transcription factor, CC-MB domain	Domain
A	IPR016071	Staphylococcal nuclease (SNase-like), OB-fold	Domain
A	IPR002999	Tudor domain	Domain
A	IPR002071	Thermonuclease active site	Active Site
A	IPR047386	Tudor domain-containing protein 11, Tudor domain	Domain
A	IPR035437	SNase-like, OB-fold superfamily	Homologous Superfamily
A	IPR016685	RNA-induced silencing complex, nuclease component Tudor-SN	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	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	Pharos: Q7KZF4	astrocytic tumor Autistic Disorder myopathy attention deficit hyperactivity disorder, inattentive type large cell medulloblastoma pancreatic ductal adenocarcinoma autism lung benign neoplasm malignant pancreatic neoplasm psoriasis

Protein Modification Annotation

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