2LD7

Solution structure of the mSin3A PAH3-SAP30 SID complex

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	SAP30_Sin3_bdg	e2ld7A1	A: alpha arrays	X: LEM/SAP HeH motif-like	H: LEM/SAP HeH motif	T: LEM/SAP HeH motif	F: SAP30_Sin3_bdg	ECOD (1.6)
B	PAH	e2ld7B1	A: alpha bundles	X: PAH2 domain (From Topology)	H: PAH2 domain (From Topology)	T: PAH2 domain	F: PAH	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	6.10.160.20	Special	Helix non-globular	Transcription Termination Factor Rho, Rna-binding Domain	Chain A, Domain 1	CATH (4.3.0)
B	1.20.1160.11	Mainly Alpha	Up-down Bundle	Paired amphipathic helix 2 (pah2 repeat)	Paired amphipathic helix	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF13866	SAP30 zinc-finger (zf-SAP30)	SAP30 zinc-finger	SAP30 is a subunit of the histone deacetylase complex, and this domain is a zinc-finger. Solution of the structure shows a novel fold comprising two beta-strands and two alpha-helices with the zinc organising centre showing remote resemblance to the ...	SAP30 is a subunit of the histone deacetylase complex, and this domain is a zinc-finger. Solution of the structure shows a novel fold comprising two beta-strands and two alpha-helices with the zinc organising centre showing remote resemblance to the treble clef motif. In silico analysis of the structure revealed a highly conserved surface dominated by basic residues. NMR-based analysis of potential ligands for the SAP30 zn-finger motif indicated a strong preference for nucleic acid substrates. The zinc-finger of SAP3 probably functions as a double-stranded DNA-binding motif, thereby expanding the known functions of both SAP30 and the mammalian Sin3 co-repressor complex [1].	Domain
A	PF13867	Sin3 binding region of histone deacetylase complex subunit SAP30 (SAP30_Sin3_bdg)	Sin3 binding region of histone deacetylase complex subunit SAP30	-	Family
B	PF02671	Paired amphipathic helix repeat (PAH)	Paired amphipathic helix repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Histone deacetylase complex subunit SAP30	DNA binding binding organic cyclic compound binding nucleic acid binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity cation binding ion binding metal ion binding small molecule binding	cellular response to stimulus negative regulation of transforming growth factor beta receptor signaling pathway regulation of cellular process cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus response to stimulus negative regulation of signaling signaling cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication regulation of transforming growth factor beta receptor signaling pathway cellular response to stimulus negative regulation of transforming growth factor beta receptor signaling pathway regulation of cellular process cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus response to stimulus negative regulation of signaling signaling cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication regulation of transforming growth factor beta receptor signaling pathway cellular response to endogenous stimulus negative regulation of cellular process signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling regulation of biological process cell surface receptor signaling pathway negative regulation of response to stimulus regulation of cellular response to transforming growth factor beta stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus biological regulation negative regulation of signal transduction response to transforming growth factor beta regulation of response to stimulus transforming growth factor beta receptor signaling pathway regulation of cell communication cellular process response to growth factor transforming growth factor beta receptor superfamily signaling pathway negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process cellular metabolic process 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 regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process biological process involved in interspecies interaction between organisms modulation by host of symbiont process biological process involved in interaction with symbiont modulation by host of symbiont transcription biological process involved in symbiotic interaction negative regulation of locomotion regulation of cell motility regulation of locomotion regulation of cell migration negative regulation of cell motility cell migration cell motility negative regulation of cell migration locomotion developmental process multicellular organismal process regulation of developmental process positive regulation of biological process regulation of stem cell population maintenance stem cell population maintenance positive regulation of developmental process positive regulation of stem cell population maintenance positive regulation of multicellular organismal process regulation of multicellular organismal process maintenance of cell number negative regulation of developmental process negative regulation of stem cell population maintenance negative regulation of multicellular organismal process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound 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 cellular biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of macromolecule metabolic process negative regulation of biosynthetic process skeletal muscle cell differentiation cellular developmental process skeletal muscle tissue development animal organ development tissue development muscle structure development skeletal muscle organ development cell differentiation anatomical structure development muscle tissue development muscle organ development	membrane-bounded organelle protein-containing complex intracellular anatomical structure Sin3-type complex nucleus membrane-enclosed lumen nuclear chromosome nuclear protein-containing complex chromosome intracellular organelle lumen histone deacetylase complex intracellular organelle nucleoplasm non-membrane-bounded organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure Sin3-type complex nucleus membrane-enclosed lumen nuclear chromosome nuclear protein-containing complex chromosome intracellular organelle lumen histone deacetylase complex intracellular organelle nucleoplasm non-membrane-bounded organelle catalytic complex protein-DNA complex chromatin intracellular membrane-bounded organelle cellular anatomical entity organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen
B	Paired amphipathic helix protein Sin3a	molecular function inhibitor activity molecular function regulator activity transcription regulator inhibitor activity DNA binding binding organic cyclic compound binding nucleic acid binding protein-containing complex binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding DNA-binding transcription factor binding chromatin binding RNA binding molecular function inhibitor activity molecular function regulator activity transcription regulator inhibitor activity DNA binding binding organic cyclic compound binding nucleic acid binding protein-containing complex binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding DNA-binding transcription factor binding chromatin binding RNA binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity	response to ketone response to organic substance response to stimulus response to chemical response to oxygen-containing compound response to methylglyoxal protein localization localization cellular localization cellular macromolecule localization macromolecule localization cellular process developmental process multicellular organismal process response to ketone response to organic substance response to stimulus response to chemical response to oxygen-containing compound response to methylglyoxal protein localization localization cellular localization cellular macromolecule localization macromolecule localization cellular process developmental process multicellular organismal process head development cellular developmental process forebrain development animal organ development brain development nervous system development generation of neurons multicellular organism development central nervous system neuron differentiation neurogenesis central nervous system development neuron differentiation cell differentiation anatomical structure development cerebral cortex neuron differentiation system development embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development cellular response to stimulus negative regulation of transforming growth factor beta receptor signaling pathway regulation of cellular process cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus negative regulation of signaling signaling cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication regulation of transforming growth factor beta receptor signaling pathway cellular response to endogenous stimulus negative regulation of cellular process signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling regulation of biological process cell surface receptor signaling pathway negative regulation of response to stimulus regulation of cellular response to transforming growth factor beta stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus biological regulation negative regulation of signal transduction response to transforming growth factor beta regulation of response to stimulus transforming growth factor beta receptor signaling pathway regulation of cell communication response to growth factor transforming growth factor beta receptor superfamily signaling pathway negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process cellular metabolic process 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 regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process negative regulation of locomotion regulation of cell motility regulation of locomotion regulation of cell migration negative regulation of cell motility cell migration cell motility negative regulation of cell migration locomotion regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus regulation of defense response to virus defense response to virus defense response to other organism response to stress regulation of response to stress positive regulation of defense response to virus by host regulation of defense response to virus by host response to external biotic stimulus response to virus regulation of developmental process negative regulation of developmental process regulation of stem cell population maintenance stem cell population maintenance negative regulation of stem cell population maintenance regulation of multicellular organismal process maintenance of cell number negative regulation of multicellular organismal process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound 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 cellular biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of macromolecule metabolic process negative regulation of biosynthetic process cellular response to nitrogen compound response to dopamine cellular response to dopamine response to monoamine response to catecholamine cellular response to catecholamine stimulus cellular response to organic substance response to organic cyclic compound response to organonitrogen compound cellular response to organic cyclic compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to organonitrogen compound cellular response to monoamine stimulus regulation of hormone levels regulation of biological quality response to cytokine cytokine-mediated signaling pathway interferon-mediated signaling pathway cellular response to type I interferon innate immune response cellular response to cytokine stimulus immune response immune system process type I interferon-mediated signaling pathway response to type I interferon DNA replication DNA metabolic process positive regulation of response to biotic stimulus positive regulation of biological process positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of immune response regulation of immune system process positive regulation of immune system process positive regulation of innate immune response regulation of innate immune response positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death homeostatic process response to monosaccharide response to carbohydrate carbohydrate homeostasis cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus cellular response to glucose stimulus intracellular glucose homeostasis response to hexose cellular response to carbohydrate stimulus cellular homeostasis chemical homeostasis response to glucose glucose homeostasis positive regulation of developmental process positive regulation of stem cell population maintenance positive regulation of multicellular organismal process rhythmic process circadian rhythm negative regulation of circadian rhythm regulation of circadian rhythm axon extension regulation of growth axonogenesis regulation of cellular component size developmental growth cell projection organization neuron projection development cell projection morphogenesis neuron projection morphogenesis developmental growth involved in morphogenesis regulation of cellular component organization plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis regulation of axon extension cellular component organization regulation of extent of cell growth cellular component organization or biogenesis regulation of cell size neuron projection extension regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth growth axon development regulation of cell growth cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron development regulation of anatomical structure size regulation of cell differentiation positive regulation of neuron differentiation positive regulation of cell differentiation positive regulation of cellular process regulation of neuron differentiation protein-DNA complex organization chromatin organization chromatin remodeling heterochromatin formation protein-containing complex organization epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic regulation of localization regulation of protein localization regulation of protein localization to nucleus protein localization to nucleus negative regulation of protein localization to nucleus regulation of cellular localization protein localization to organelle negative regulation of protein localization hemopoiesis hematopoietic progenitor cell differentiation regulation of cell cycle phase transition G2/M transition of mitotic cell cycle cell cycle phase transition mitotic cell cycle regulation of mitotic cell cycle positive regulation of mitotic cell cycle phase transition positive regulation of cell cycle process positive regulation of mitotic cell cycle cell cycle regulation of cell cycle cell cycle process cell cycle G2/M phase transition positive regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process regulation of cell cycle G2/M phase transition positive regulation of cell cycle G2/M phase transition positive regulation of cell cycle regulation of mitotic cell cycle phase transition mitotic cell cycle process positive regulation of cell cycle phase transition mitotic cell cycle phase transition	protein-containing complex transcription regulator complex intracellular organelle intracellular anatomical structure protein-DNA complex organelle intracellular non-membrane-bounded organelle chromatin chromosome cellular anatomical entity non-membrane-bounded organelle membrane-bounded organelle nucleus membrane-enclosed lumen protein-containing complex transcription regulator complex intracellular organelle intracellular anatomical structure protein-DNA complex organelle intracellular non-membrane-bounded organelle chromatin chromosome cellular anatomical entity non-membrane-bounded organelle membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen organelle lumen nuclear lumen Sin3-type complex nuclear chromosome nuclear protein-containing complex histone deacetylase complex nucleoplasm catalytic complex chromosomal region kinetochore chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome transcription repressor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR038291	SAP30, C-terminal domain superfamily	Homologous Superfamily
A	IPR025717	Histone deacetylase complex subunit SAP30 zinc-finger	Domain
A	IPR025718	Histone deacetylase complex subunit SAP30, Sin3 binding domain	Domain
A	IPR024145	Histone deacetylase complex subunit SAP30/SAP30-like	Family
B	IPR013194	Histone deacetylase interacting domain	Domain
B	IPR039774	Transcriptional regulatory protein Sin3-like	Family
B	IPR003822	Paired amphipathic helix	Repeat
B	IPR036600	Paired amphipathic helix superfamily	Homologous Superfamily
B	IPR031693	Sin3, C-terminal	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.