8BPC

Cryo-EM structure of the human SIN3B histone deacetylase core complex with SAHA at 2.8 Angstrom

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Arginase/deacetylase-like	8088484	3000260	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)
B	PF00850	e8bpcB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: PF00850	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02671	Paired amphipathic helix repeat (PAH)	Paired amphipathic helix repeat	-	Repeat
A	PF16879	C-terminal domain of Sin3a protein (Sin3a_C)	C-terminal domain of Sin3a protein	-	Family
B	PF00850	Histone deacetylase domain (Hist_deacetyl)	Histone deacetylase domain	Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1]. ...	Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1].	Domain
C	PF00628	PHD-finger (PHD)	PHD-finger	PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2]. Several PHD fingers have been identified as binding modules of methylated histone H3 [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Isoform 2 of Paired amphipathic helix protein Sin3b	transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity protein-containing complex binding chromatin binding binding	negative regulation of locomotion regulation of biological process regulation of cell motility regulation of cellular process biological regulation negative regulation of biological process regulation of locomotion negative regulation of cellular process regulation of cell migration negative regulation of cell motility cellular process cell migration cell motility negative regulation of cell migration negative regulation of locomotion regulation of biological process regulation of cell motility regulation of cellular process biological regulation negative regulation of biological process regulation of locomotion negative regulation of cellular process regulation of cell migration negative regulation of cell motility cellular process cell migration cell motility negative regulation of cell migration locomotion negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process 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 cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic 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 negative regulation of biosynthetic process	intracellular organelle intracellular anatomical structure sex chromosome organelle intracellular non-membrane-bounded organelle chromosome cellular anatomical entity non-membrane-bounded organelle X chromosome Y chromosome membrane-bounded organelle protein-containing complex Sin3-type complex nucleus intracellular organelle intracellular anatomical structure sex chromosome organelle intracellular non-membrane-bounded organelle chromosome cellular anatomical entity non-membrane-bounded organelle X chromosome Y chromosome membrane-bounded organelle protein-containing complex Sin3-type complex nucleus membrane-enclosed lumen nuclear chromosome nuclear protein-containing complex intracellular organelle lumen histone deacetylase complex nucleoplasm catalytic complex protein-DNA complex chromatin intracellular membrane-bounded organelle organelle lumen nuclear lumen XY body cytoplasm autosome
B	Histone deacetylase 2	protein binding binding histone binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding NF-kappaB binding histone deacetylase binding enzyme binding heat shock protein binding deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein hydrolase activity protein binding binding histone binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding NF-kappaB binding histone deacetylase binding enzyme binding heat shock protein binding deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein hydrolase activity catalytic activity protein-containing complex binding chromatin binding promoter-specific chromatin binding histone deacetylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides histone modifying activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds protein de-2-hydroxyisobutyrylase activity RNA binding organic cyclic compound binding nucleic acid binding protein decrotonylase activity histone decrotonylase activity	response to stimulus response to chemical response to xenobiotic stimulus multicellular organismal process regulation of cellular process interleukin-1 production cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process regulation of cytokine production response to stimulus response to chemical response to xenobiotic stimulus multicellular organismal process regulation of cellular process interleukin-1 production cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process regulation of cytokine production organic substance biosynthetic process cytokine production positive regulation of interleukin-1 production regulation of multicellular organismal process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process regulation of interleukin-1 production cellular metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process positive regulation of cellular biosynthetic process organonitrogen compound metabolic process macromolecule modification primary metabolic process protein metabolic process protein modification process developmental process regulation of developmental process cellular developmental process regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation cellular response to stimulus cellular response to heat cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus response to organic substance response to organonitrogen compound response to nitrogen compound response to purine-containing compound response to organic cyclic compound response to caffeine response to alkaloid negative regulation of biological process regulation of MHC class II biosynthetic process negative regulation of MHC class II biosynthetic process negative regulation of cellular metabolic process MHC class II biosynthetic process negative regulation of cellular process negative regulation of macromolecule metabolic process negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process response to lipid response to oxygen-containing compound cellular response to oxygen-containing compound response to retinoic acid cellular response to chemical stimulus cellular response to retinoic acid cellular response to lipid cellular response to organic substance regulation of neuron projection development regulation of cellular component organization cell projection organization cell development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation anatomical structure development cellular component organization or biogenesis negative regulation of cell projection organization system development plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization nervous system development negative regulation of neuron projection development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization rhythmic process circadian regulation of gene expression circadian rhythm positive regulation of protein metabolic process regulation of protein metabolic process regulation of primary metabolic process regulation of proteolysis proteolysis positive regulation of proteolysis regulation of signaling signaling positive regulation of signaling receptor activity regulation of signaling receptor activity regulation of signal transduction cell communication positive regulation of molecular function regulation of molecular function regulation of response to stimulus regulation of cell communication signal transduction negative regulation of transforming growth factor beta receptor signaling pathway cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus negative regulation of signaling cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of cell communication regulation of transforming growth factor beta receptor signaling pathway cellular response to endogenous stimulus enzyme-linked receptor protein signaling pathway 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 negative regulation of signal transduction response to transforming growth factor beta transforming growth factor beta receptor signaling pathway response to growth factor transforming growth factor beta receptor superfamily signaling pathway negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 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 epithelium development epidermal cell differentiation epidermis development tissue development epithelial cell differentiation negative regulation of developmental process regulation of stem cell population maintenance stem cell population maintenance negative regulation of stem cell population maintenance maintenance of cell number negative regulation of multicellular organismal process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process 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 organic cyclic compound metabolic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process collagen biosynthetic process regulation of collagen biosynthetic process regulation of collagen metabolic process positive regulation of collagen metabolic process positive regulation of collagen biosynthetic process collagen metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of RNA 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 cyclic compound cellular response to organonitrogen compound cellular response to monoamine stimulus negative regulation of dendritic spine development regulation of dendritic spine development dendrite development dendritic spine development ectodermal placode morphogenesis molting cycle process hair cycle animal organ development hair follicle placode formation ectodermal placode formation anatomical structure morphogenesis skin development skin epidermis development hair follicle development molting cycle anatomical structure formation involved in morphogenesis ectodermal placode development hair cycle process negative regulation of DNA-binding transcription factor activity negative regulation of molecular function regulation of DNA-binding transcription factor activity regulation of cell fate commitment cell fate specification regulation of cell fate specification cell fate commitment odontogenesis of dentin-containing tooth odontogenesis animal organ morphogenesis 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 regulation of epithelial to mesenchymal transition positive regulation of epithelial to mesenchymal transition mesenchyme development positive regulation of developmental process positive regulation of cell differentiation epithelial to mesenchymal transition mesenchymal cell differentiation positive regulation of stem cell population maintenance behavior adult behavior response to alcohol behavioral response to ethanol response to ethanol cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation response to amyloid-beta cellular response to oxidative stress cellular response to chemical stress cellular response to hydrogen peroxide response to reactive oxygen species response to inorganic substance response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species negative regulation of transcription by competitive promoter binding positive regulation of phosphorylation positive regulation of phosphate metabolic process regulation of phosphate metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process phosphorus metabolic process positive regulation of protein phosphorylation tyrosine phosphorylation of STAT protein protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of phosphorus metabolic process cell surface receptor signaling pathway via STAT regulation of protein modification process regulation of protein phosphorylation peptidyl-tyrosine modification positive regulation of peptidyl-tyrosine phosphorylation positive regulation of protein modification process regulation of tyrosine phosphorylation of STAT protein regulation of peptidyl-tyrosine phosphorylation positive regulation of tyrosine phosphorylation of STAT protein regulation of phosphorylation peptidyl-tyrosine phosphorylation cell surface receptor signaling pathway via JAK-STAT muscle hypertrophy system process cardiac muscle hypertrophy striated muscle hypertrophy muscle system process 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 peptidyl-lysine acetylation peptidyl-lysine modification protein acylation negative regulation of protein modification process negative regulation of protein metabolic process negative regulation of protein acetylation negative regulation of peptidyl-lysine acetylation protein acetylation regulation of protein acetylation regulation of peptidyl-lysine acetylation response to amine response to amphetamine positive regulation of nervous system development regulation of neurogenesis regulation of gliogenesis positive regulation of gliogenesis regulation of cell development regulation of nervous system development gliogenesis positive regulation of neurogenesis positive regulation of oligodendrocyte differentiation regulation of multicellular organismal development regulation of glial cell differentiation positive regulation of cell development positive regulation of glial cell differentiation central nervous system development oligodendrocyte differentiation glial cell differentiation regulation of oligodendrocyte differentiation eyelid development in camera-type eye sensory organ development eye development visual system development camera-type eye development sensory system development regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production response to nicotine tongue development fungiform papilla formation fungiform papilla development sensory organ morphogenesis fungiform papilla morphogenesis tongue morphogenesis regulation of reproductive process reproductive process male mating behavior multicellular organismal reproductive process mating behavior positive regulation of male mating behavior regulation of behavior positive regulation of behavior reproductive behavior regulation of male mating behavior positive regulation of reproductive process 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 response to cocaine limb development appendage development embryonic limb morphogenesis embryonic morphogenesis embryonic appendage morphogenesis embryo development appendage morphogenesis embryonic digit morphogenesis limb morphogenesis response to oxygen levels response to hyperoxia response to increased oxygen levels	membrane-bounded organelle protein-containing complex histone methyltransferase complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex intracellular organelle lumen PcG protein complex intracellular organelle membrane-bounded organelle protein-containing complex histone methyltransferase complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex intracellular organelle lumen PcG protein complex intracellular organelle nucleoplasm organelle lumen organelle methyltransferase complex ESC/E(Z) complex nuclear lumen cytoplasm protein-DNA complex intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle ATPase complex transcription regulator complex histone deacetylase complex NuRD complex SWI/SNF superfamily-type complex CHD-type complex chromosome, telomeric region chromosomal region Sin3-type complex nuclear chromosome
C	PHD finger protein 12	binding phospholipid binding lipid binding phosphatidylinositol binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding transcription coregulator binding transcription corepressor binding protein binding cation binding binding phospholipid binding lipid binding phosphatidylinositol binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding transcription coregulator binding transcription corepressor binding protein binding cation binding ion binding metal ion binding small molecule binding	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II	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 transcription regulator complex transcription repressor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR039774	Transcriptional regulatory protein Sin3-like	Family
A	IPR031693	Sin3, C-terminal	Domain
A	IPR013194	Histone deacetylase interacting domain	Domain
A	IPR003822	Paired amphipathic helix	Repeat
A	IPR036600	Paired amphipathic helix superfamily	Homologous Superfamily
B	IPR000286	Histone deacetylase family	Family
B	IPR023801	Histone deacetylase domain	Domain
B	IPR003084	Histone deacetylase	Family
B	IPR037138	Histone deacetylase domain superfamily	Homologous Superfamily
B	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily
C	IPR001965	Zinc finger, PHD-type	Domain
C	IPR008984	SMAD/FHA domain superfamily	Homologous Superfamily
C	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
C	IPR000253	Forkhead-associated (FHA) domain	Domain
C	IPR019787	Zinc finger, PHD-finger	Domain
C	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
C	IPR031966	PHD finger protein 12, MRG binding domain	Domain
C	IPR038098	PHD finger protein 12, MRG binding domain superfamily	Homologous Superfamily
C	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O75182	breast cancer osteosarcoma Pick disease
B	Pharos: Q92769	myeloid leukemia squamous cell carcinoma melanoma Microsatellite Instability chronic monocytic leukemia cirrhosis of liver endometriosis plasma cell myeloma prostate adenocarcinoma acute T cell leukemia schizophrenia cancer chronic obstructive pulmonary disease large cell medulloblastoma medulloblastoma myeloid leukemia squamous cell carcinoma melanoma Microsatellite Instability chronic monocytic leukemia cirrhosis of liver endometriosis plasma cell myeloma prostate adenocarcinoma acute T cell leukemia schizophrenia cancer chronic obstructive pulmonary disease large cell medulloblastoma medulloblastoma primary cutaneous T-cell lymphoma adult T-cell leukemia/lymphoma lung cancer ovarian cancer primitive neuroectodermal tumor cutaneous melanoma mature T-cell and NK-cell non-Hodgkin lymphoma
C	Pharos: Q96QT6	acute myeloid leukemia endogenous depression large cell medulloblastoma ovarian cancer atypical teratoid rhabdoid tumor glioblastoma medulloblastoma primitive neuroectodermal tumor bipolar disorder juvenile dermatomyositis osteosarcoma

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 R01GM133198.