8W9C

Cryo-EM structure of the Rpd3S complex from budding yeast

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF08295	Sin3 family co-repressor (Sin3_corepress)	Sin3 family co-repressor	This domain is found on transcriptional regulators. It forms interactions with histone deacetylases [1].	Domain
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 [auth E], F	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
C [auth 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Transcriptional regulatory protein SIN3	transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription corepressor activity identical protein binding protein binding binding	regulation of cellular process negative regulation of biological process negative regulation of heterochromatin formation positive regulation of macromolecule biosynthetic process negative regulation of cellular metabolic process positive regulation of metabolic process chromatin organization positive regulation of macromolecule metabolic process regulation of heterochromatin formation regulation of biological process regulation of chromatin organization negative regulation of cellular component organization cellular metabolic process negative regulation of metabolic process regulation of cellular process negative regulation of biological process negative regulation of heterochromatin formation positive regulation of macromolecule biosynthetic process negative regulation of cellular metabolic process positive regulation of metabolic process chromatin organization positive regulation of macromolecule metabolic process regulation of heterochromatin formation regulation of biological process regulation of chromatin organization negative regulation of cellular component organization cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation biosynthetic process negative regulation of macromolecule biosynthetic process silent mating-type cassette heterochromatin formation negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of cellular component organization cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process negative regulation of chromatin organization protein-DNA complex organization cellular component organization positive regulation of biosynthetic process negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process heterochromatin formation negative regulation of silent mating-type cassette heterochromatin formation protein-containing complex organization epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of silent mating-type cassette heterochromatin formation negative regulation of biosynthetic process positive regulation of gene expression cellular process positive regulation of cellular biosynthetic process regulation of rDNA heterochromatin formation rDNA heterochromatin formation nucleolus organization nucleolar chromatin organization negative regulation of rDNA heterochromatin formation nucleus organization organelle organization facultative heterochromatin formation cell division cellular catabolic process catabolic process macroautophagy autophagy nucleophagy process utilizing autophagic mechanism rDNA chromatin condensation chromosome organization chromosome condensation regulation of DNA-templated DNA replication initiation DNA-templated DNA replication DNA replication initiation primary metabolic process DNA metabolic process nucleic acid metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process DNA replication regulation of DNA-templated DNA replication regulation of nucleobase-containing compound metabolic process regulation of DNA replication regulation of DNA metabolic process cell cycle protein-DNA complex assembly cellular component biogenesis cellular component assembly protein-containing complex assembly nucleosome assembly nucleosome organization RNA metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process regulation of DNA-templated transcription negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of RNA metabolic process positive regulation of DNA-templated transcription 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 RNA biosynthetic process negative regulation of transcription by RNA polymerase I transcription by RNA polymerase I regulation of transcription by RNA polymerase I cellular response to stimulus double-strand break repair response to stimulus double-strand break repair via nonhomologous end joining cellular response to stress DNA damage response response to stress DNA repair	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 Rpd3L-Expanded complex Rpd3S complex Rpd3L complex
B [auth E], F	Transcriptional regulatory protein RCO1	cation binding ion binding binding metal ion binding small molecule binding	protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization regulation of cellular process protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization 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 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 regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription antisense RNA metabolic process regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process regulation of antisense RNA transcription RNA biosynthetic process nucleic acid biosynthetic 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 negative regulation of antisense RNA transcription macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process antisense RNA transcription transcription elongation by RNA polymerase II DNA-templated transcription elongation transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II positive regulation of DNA-templated transcription 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 nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process regulation of DNA-templated DNA replication initiation DNA-templated DNA replication DNA replication initiation DNA metabolic process DNA replication regulation of DNA-templated DNA replication regulation of DNA replication regulation of DNA metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure Sin3-type complex nucleus membrane-enclosed lumen nuclear chromosome nuclear protein-containing complex Rpd3S complex chromosome intracellular organelle lumen histone deacetylase complex intracellular organelle nucleoplasm membrane-bounded organelle protein-containing complex intracellular anatomical structure Sin3-type complex nucleus membrane-enclosed lumen nuclear chromosome nuclear protein-containing complex Rpd3S 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
C [auth B]	Histone deacetylase RPD3	transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription corepressor activity deacetylase activity histone deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity histone modifying activity catalytic activity transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription corepressor activity deacetylase activity histone deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity histone modifying activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	regulation of cellular process negative regulation of biological process negative regulation of heterochromatin formation positive regulation of macromolecule biosynthetic process negative regulation of cellular metabolic process positive regulation of metabolic process chromatin organization positive regulation of macromolecule metabolic process regulation of heterochromatin formation regulation of biological process regulation of chromatin organization negative regulation of cellular component organization cellular metabolic process negative regulation of metabolic process regulation of cellular process negative regulation of biological process negative regulation of heterochromatin formation positive regulation of macromolecule biosynthetic process negative regulation of cellular metabolic process positive regulation of metabolic process chromatin organization positive regulation of macromolecule metabolic process regulation of heterochromatin formation regulation of biological process regulation of chromatin organization negative regulation of cellular component organization cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation biosynthetic process negative regulation of macromolecule biosynthetic process silent mating-type cassette heterochromatin formation negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of cellular component organization cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process negative regulation of chromatin organization protein-DNA complex organization cellular component organization positive regulation of biosynthetic process negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process heterochromatin formation negative regulation of silent mating-type cassette heterochromatin formation protein-containing complex organization epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of silent mating-type cassette heterochromatin formation negative regulation of biosynthetic process positive regulation of gene expression cellular process positive regulation of cellular biosynthetic process regulation of rDNA heterochromatin formation rDNA heterochromatin formation nucleolus organization nucleolar chromatin organization negative regulation of rDNA heterochromatin formation nucleus organization organelle organization facultative heterochromatin formation cellular catabolic process catabolic process macroautophagy autophagy nucleophagy process utilizing autophagic mechanism rDNA chromatin condensation chromosome organization chromosome condensation regulation of DNA-templated DNA replication initiation DNA-templated DNA replication DNA replication initiation primary metabolic process DNA metabolic process nucleic acid metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process DNA replication regulation of DNA-templated DNA replication regulation of nucleobase-containing compound metabolic process regulation of DNA replication regulation of DNA metabolic process protein-DNA complex assembly cellular component biogenesis cellular component assembly protein-containing complex assembly nucleosome assembly nucleosome organization regulation of DNA recombination homologous recombination regulation of reproductive process negative regulation of cell cycle negative regulation of nucleobase-containing compound metabolic process cell cycle reciprocal homologous recombination regulation of meiotic cell cycle regulation of cell cycle process DNA recombination meiotic cell cycle regulation of organelle organization negative regulation of DNA recombination reciprocal meiotic recombination meiosis I cell cycle process negative regulation of meiotic cell cycle sexual reproduction negative regulation of reciprocal meiotic recombination reproductive process meiotic cell cycle process meiosis I regulation of reciprocal meiotic recombination meiotic nuclear division regulation of cell cycle negative regulation of meiotic nuclear division cell cycle process organelle fission negative regulation of cell cycle process regulation of meiotic nuclear division nuclear division negative regulation of nuclear division negative regulation of organelle organization negative regulation of reproductive process regulation of nuclear division negative regulation of DNA metabolic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process regulation of DNA-templated transcription regulation of autophagy positive regulation of macroautophagy positive regulation of autophagy regulation of catabolic process positive regulation of catabolic process regulation of macroautophagy regulation of cellular catabolic process positive regulation of cellular catabolic process protein localization cellular localization protein localization to nucleolar rDNA repeats localization protein localization to chromosome protein localization to organelle cellular macromolecule localization macromolecule localization transcription elongation by RNA polymerase II DNA-templated transcription elongation transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of RNA biosynthetic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of RNA metabolic process response to oxidative stress response to stimulus response to stress positive regulation of DNA-templated transcription 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 RNA biosynthetic process negative regulation of transcription by RNA polymerase I transcription by RNA polymerase I regulation of transcription by RNA polymerase I	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 Rpd3L-Expanded complex nuclear periphery cytoplasm ATPase complex transcription regulator complex NuRD complex SWI/SNF superfamily-type complex CHD-type complex Snt2C complex Rpd3S complex Rpd3L complex
D [auth C], E [auth D]	Chromatin modification-related protein EAF3	-	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 protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular component organization or biogenesis nucleosome assembly nucleosome organization catabolic process macromolecule catabolic process post-transcriptional regulation of gene expression regulation of biological quality RNA catabolic process regulation of catabolic process nucleobase-containing compound catabolic process regulation of RNA stability nucleic acid catabolic process antisense RNA metabolic process regulation of antisense RNA transcription negative regulation of antisense RNA transcription antisense RNA transcription cellular response to stimulus response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair DNA replication-dependent chromatin assembly transcription elongation by RNA polymerase II DNA-templated transcription elongation transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of DNA-templated transcription elongation positive regulation of nucleobase-containing compound metabolic process regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation positive regulation of cellular process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process negative regulation of transcription by RNA polymerase II cellular component disassembly protein-DNA complex disassembly protein-containing complex disassembly nucleosome disassembly regulation of DNA-templated DNA replication initiation DNA-templated DNA replication DNA replication initiation DNA replication regulation of DNA-templated DNA replication regulation of DNA replication regulation of DNA metabolic process	protein-containing complex intracellular anatomical structure catalytic complex protein-DNA complex chromatin chromosome transferase complex cellular anatomical entity histone acetyltransferase complex acetyltransferase complex intracellular organelle organelle intracellular non-membrane-bounded organelle protein acetyltransferase complex protein-containing complex intracellular anatomical structure catalytic complex protein-DNA complex chromatin chromosome transferase complex cellular anatomical entity histone acetyltransferase complex acetyltransferase complex intracellular organelle organelle intracellular non-membrane-bounded organelle protein acetyltransferase complex intracellular protein-containing complex non-membrane-bounded organelle NuA4 histone acetyltransferase complex H4/H2A histone acetyltransferase complex H4 histone acetyltransferase complex membrane-bounded organelle Sin3-type complex nucleus membrane-enclosed lumen nuclear chromosome nuclear protein-containing complex Rpd3S complex intracellular organelle lumen histone deacetylase complex nucleoplasm intracellular membrane-bounded organelle organelle lumen nuclear lumen nucleosome disassembly/reassembly complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR039774	Transcriptional regulatory protein Sin3-like	Family
A	IPR013194	Histone deacetylase interacting domain	Domain
A	IPR003822	Paired amphipathic helix	Repeat
A	IPR036600	Paired amphipathic helix superfamily	Homologous Superfamily
A	IPR031693	Sin3, C-terminal	Domain
B [auth E], F	IPR001965	Zinc finger, PHD-type	Domain
B [auth E], F	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B [auth E], F	IPR019787	Zinc finger, PHD-finger	Domain
B [auth E], F	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
B [auth E], F	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
C [auth B]	IPR000286	Histone deacetylase family	Family
C [auth B]	IPR023801	Histone deacetylase domain	Domain
C [auth B]	IPR003084	Histone deacetylase	Family
C [auth B]	IPR037138	Histone deacetylase domain superfamily	Homologous Superfamily
C [auth B]	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily
D [auth C], E [auth D]	IPR000953	Chromo/chromo shadow domain	Domain
D [auth C], E [auth D]	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
D [auth C], E [auth D]	IPR025995	RNA binding activity-knot of a chromodomain	Domain
D [auth C], E [auth D]	IPR008676	MRG	Family
D [auth C], E [auth D]	IPR026541	MRG domain	Domain
D [auth C], E [auth D]	IPR038217	MRG, C-terminal domain superfamily	Homologous Superfamily

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.

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8W9C

Cryo-EM structure of the Rpd3S complex from budding yeast

External Resource: Annotation

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage