Annotations: 9V2W

Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with di-nucleosome

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Gene Ontology: Gene Product Annotation
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Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I	Transcriptional regulatory protein PHO23	histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity protein-macromolecule adaptor activity molecular adaptor activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex 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 cellular component organization protein-DNA complex 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 heterochromatin formation positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of heterochromatin formation regulation of biological process regulation of chromatin organization negative regulation of cellular component organization negative regulation of metabolic process heterochromatin organization 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 positive regulation of biological process negative regulation of chromatin organization positive regulation of biosynthetic process negative regulation of cellular process 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 epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of silent mating-type cassette heterochromatin formation negative regulation of biosynthetic process positive regulation of gene expression regulation of heterochromatin organization negative regulation of heterochromatin organization 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 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 regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription positive regulation of invasive growth in response to glucose limitation regulation of growth regulation of growth of unicellular organism as a thread of attached cells growth regulation of filamentous growth of a population of unicellular organisms positive regulation of growth of unicellular organism as a thread of attached cells filamentous growth positive regulation of filamentous growth of a population of unicellular organisms regulation of invasive growth in response to glucose limitation filamentous growth of a population of unicellular organisms positive regulation of growth regulation of filamentous growth invasive growth in response to glucose limitation positive regulation of filamentous growth growth of unicellular organism as a thread of attached cells invasive filamentous growth cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus transcription by RNA polymerase II regulation of transcription by RNA polymerase II 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 negative regulation of RNA biosynthetic process negative regulation of transcription by RNA polymerase I transcription by RNA polymerase I negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of transcription by RNA polymerase I negative regulation of RNA metabolic process	membrane-bounded organelle Rpd3L-Expanded complex protein-containing complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular membrane-bounded organelle intracellular organelle lumen membrane-bounded organelle Rpd3L-Expanded complex protein-containing complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular membrane-bounded organelle intracellular organelle lumen histone deacetylase complex intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle nuclear lumen Sin3-type complex Rpd3L complex
H, Q, U, W	Histone H3	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
G	Transcriptional regulatory protein SAP30	transcription corepressor activity transcription regulator activity transcription coregulator activity	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex 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 cellular component organization protein-DNA complex 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 heterochromatin formation positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of heterochromatin formation regulation of biological process regulation of chromatin organization negative regulation of cellular component organization negative regulation of metabolic process heterochromatin organization 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 positive regulation of biological process negative regulation of chromatin organization positive regulation of biosynthetic process negative regulation of cellular process 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 epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of silent mating-type cassette heterochromatin formation negative regulation of biosynthetic process positive regulation of gene expression regulation of heterochromatin organization negative regulation of heterochromatin organization 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 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 regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription positive regulation of invasive growth in response to glucose limitation regulation of growth regulation of growth of unicellular organism as a thread of attached cells growth regulation of filamentous growth of a population of unicellular organisms positive regulation of growth of unicellular organism as a thread of attached cells filamentous growth positive regulation of filamentous growth of a population of unicellular organisms regulation of invasive growth in response to glucose limitation filamentous growth of a population of unicellular organisms positive regulation of growth regulation of filamentous growth invasive growth in response to glucose limitation positive regulation of filamentous growth growth of unicellular organism as a thread of attached cells invasive filamentous growth cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus transcription by RNA polymerase II regulation of transcription by RNA polymerase II 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 negative regulation of RNA biosynthetic process negative regulation of transcription by RNA polymerase I transcription by RNA polymerase I negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of transcription by RNA polymerase I negative regulation of RNA metabolic process	membrane-bounded organelle Rpd3L-Expanded complex protein-containing complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular membrane-bounded organelle intracellular organelle lumen membrane-bounded organelle Rpd3L-Expanded complex protein-containing complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular membrane-bounded organelle intracellular organelle lumen histone deacetylase complex intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle nuclear lumen Sin3-type complex Rpd3L complex
F	Transcriptional regulatory protein SDS3	histone deacetylase binding protein binding binding enzyme binding	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex 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 cellular component organization protein-DNA complex 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 heterochromatin formation positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of heterochromatin formation regulation of biological process regulation of chromatin organization negative regulation of cellular component organization negative regulation of metabolic process heterochromatin organization 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 positive regulation of biological process negative regulation of chromatin organization positive regulation of biosynthetic process negative regulation of cellular process 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 epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of silent mating-type cassette heterochromatin formation negative regulation of biosynthetic process positive regulation of gene expression regulation of heterochromatin organization negative regulation of heterochromatin organization 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 response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus 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 transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription regulation of growth regulation of growth of unicellular organism as a thread of attached cells growth regulation of filamentous growth of a population of unicellular organisms filamentous growth regulation of invasive growth in response to glucose limitation filamentous growth of a population of unicellular organisms regulation of filamentous growth invasive growth in response to glucose limitation growth of unicellular organism as a thread of attached cells invasive filamentous growth 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 transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process cell adhesion involved in biofilm formation cell aggregation biofilm formation biological process involved in intraspecies interaction between organisms cell-substrate adhesion single-species biofilm formation aggregation of unicellular organisms submerged biofilm formation cell adhesion involved in single-species biofilm formation cell adhesion single-species submerged biofilm formation	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex Sin3-type complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular membrane-bounded organelle intracellular organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex Sin3-type complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular membrane-bounded organelle intracellular organelle lumen histone deacetylase complex intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle nuclear lumen cytoplasm cytosol Rpd3L-Expanded complex Rpd3L complex
E	Transcriptional regulatory protein DEP1	histone deacetylase binding protein binding binding enzyme binding	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex 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 cellular component organization protein-DNA complex 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 heterochromatin formation positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of heterochromatin formation regulation of biological process regulation of chromatin organization negative regulation of cellular component organization negative regulation of metabolic process heterochromatin organization 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 positive regulation of biological process negative regulation of chromatin organization positive regulation of biosynthetic process negative regulation of cellular process 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 epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of silent mating-type cassette heterochromatin formation negative regulation of biosynthetic process positive regulation of gene expression regulation of heterochromatin organization negative regulation of heterochromatin organization 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 positive regulation of inositol biosynthetic process alcohol metabolic process regulation of inositol biosynthetic process regulation of small molecule metabolic process polyol biosynthetic process small molecule metabolic process polyol metabolic process regulation of alcohol biosynthetic process small molecule biosynthetic process inositol biosynthetic process inositol metabolic process alcohol biosynthetic process positive regulation of small molecule metabolic process positive regulation of alcohol biosynthetic process cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus regulation of lipid metabolic process glycerophospholipid metabolic process modified amino acid biosynthetic process lipid biosynthetic process negative regulation of phosphate metabolic process negative regulation of lipid biosynthetic process regulation of primary metabolic process phospholipid metabolic process phosphate-containing compound metabolic process negative regulation of phospholipid biosynthetic process regulation of phosphatidylserine biosynthetic process phosphorus metabolic process phosphatidylserine metabolic process negative regulation of phosphatidylserine biosynthetic process glycerophospholipid biosynthetic process modified amino acid metabolic process regulation of phospholipid metabolic process primary metabolic process phosphatidylserine biosynthetic process phospholipid biosynthetic process regulation of phospholipid biosynthetic process negative regulation of phospholipid metabolic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process negative regulation of phosphorus metabolic process glycerolipid metabolic process regulation of phosphorus metabolic process regulation of lipid biosynthetic process negative regulation of lipid metabolic process lipid metabolic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription positive regulation of phosphate metabolic process positive regulation of lipid metabolic process positive regulation of phosphorus metabolic process positive regulation of phospholipid biosynthetic process positive regulation of phospholipid metabolic process positive regulation of phosphatidylserine biosynthetic process positive regulation of lipid biosynthetic process 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 negative regulation of small molecule metabolic process negative regulation of inositol biosynthetic process negative regulation of alcohol biosynthetic process 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 negative regulation of phosphatidylcholine biosynthetic process phosphatidylcholine metabolic process regulation of phosphatidylcholine metabolic process phosphatidylcholine biosynthetic process regulation of phosphatidylcholine biosynthetic process positive regulation of phosphatidylcholine 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 intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex Sin3-type complex nucleus membrane-enclosed lumen nuclear protein-containing complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex Sin3-type complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular organelle lumen histone deacetylase complex nucleoplasm organelle lumen membraneless organelle nuclear lumen Rpd3L-Expanded complex Rpd3L complex
D, N, P, T	Histone H2B	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
C	Histone deacetylase RPD3	transcription coactivator activity transcription regulator activity transcription coregulator activity transcription corepressor activity deacetylase activity histone deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein deacylase activity histone modifying activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds transcription coactivator activity transcription regulator activity transcription coregulator activity transcription corepressor activity deacetylase activity histone deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein deacylase activity histone modifying activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds histone deacetylase activity, hydrolytic mechanism	regulation of cellular process negative regulation of biological process negative regulation of heterochromatin formation positive regulation of macromolecule biosynthetic process cellular component biogenesis positive regulation of metabolic process cellular component assembly 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 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 cellular component biogenesis positive regulation of metabolic process cellular component assembly 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 negative regulation of metabolic process heterochromatin organization 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 positive regulation of biological process negative regulation of chromatin 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 epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of silent mating-type cassette heterochromatin formation negative regulation of biosynthetic process positive regulation of gene expression regulation of heterochromatin organization cellular process negative regulation of heterochromatin organization 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 response to stimulus response to nutrient levels cellular response to nitrogen levels response to stimulus cellular response to starvation cellular response to nutrient levels cellular response to stress cellular response to nitrogen starvation response to stress response to starvation cellular response to heat response to heat response to abiotic stimulus response to temperature stimulus 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-containing complex organization protein-DNA complex assembly protein-DNA complex organization 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 positive regulation of autophagy regulation of catabolic process regulation of autophagy positive regulation of catabolic process regulation of macroautophagy positive regulation of macroautophagy protein localization to nucleolar rDNA repeats localization protein localization to chromosome protein localization to organelle macromolecule localization intracellular protein localization mitotic cell cycle process cell cycle phase transition G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition 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 cell cycle G2/M phase transition G2/M transition of mitotic cell cycle 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 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 catalytic complex Sin3-type complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular membrane-bounded organelle intracellular organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex Sin3-type complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular membrane-bounded organelle intracellular organelle lumen histone deacetylase complex intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle nuclear lumen Rpd3L-Expanded complex nuclear periphery cytoplasm Snt2C complex Rpd3S complex Rpd3L complex
B, M, O, S	Histone H2A	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process cellular process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
Z [auth Y]	DNA (329-MER)	-	-	-
Y [auth X]	DNA (329-MER)	-	-	-
L, R, V, X [auth Z]	Histone H4	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex 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	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
K	Histone deacetylase complex subunit CTI6	histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity protein-macromolecule adaptor activity molecular adaptor activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex 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 cellular component organization protein-DNA complex 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 heterochromatin formation positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of heterochromatin formation regulation of biological process regulation of chromatin organization negative regulation of cellular component organization negative regulation of metabolic process heterochromatin organization 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 positive regulation of biological process negative regulation of chromatin organization positive regulation of biosynthetic process negative regulation of cellular process 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 epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of silent mating-type cassette heterochromatin formation negative regulation of biosynthetic process positive regulation of gene expression regulation of heterochromatin organization negative regulation of heterochromatin organization 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 positive regulation of DNA-templated transcription 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 regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription transcription by RNA polymerase II regulation of transcription by RNA polymerase II 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 Rpd3L-Expanded complex protein-containing complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular membrane-bounded organelle intracellular organelle lumen membrane-bounded organelle Rpd3L-Expanded complex protein-containing complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular membrane-bounded organelle intracellular organelle lumen histone deacetylase complex intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle nuclear lumen Sin3-type complex Rpd3L complex
J	Transcriptional regulatory protein RXT2	-	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex 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 cellular component organization protein-DNA complex 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 heterochromatin formation positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of heterochromatin formation regulation of biological process regulation of chromatin organization negative regulation of cellular component organization negative regulation of metabolic process heterochromatin organization 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 positive regulation of biological process negative regulation of chromatin organization positive regulation of biosynthetic process negative regulation of cellular process 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 epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of silent mating-type cassette heterochromatin formation negative regulation of biosynthetic process positive regulation of gene expression regulation of heterochromatin organization negative regulation of heterochromatin organization 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 positive regulation of invasive growth in response to glucose limitation regulation of growth regulation of growth of unicellular organism as a thread of attached cells growth regulation of filamentous growth of a population of unicellular organisms positive regulation of growth of unicellular organism as a thread of attached cells filamentous growth positive regulation of filamentous growth of a population of unicellular organisms regulation of invasive growth in response to glucose limitation filamentous growth of a population of unicellular organisms positive regulation of growth regulation of filamentous growth invasive growth in response to glucose limitation positive regulation of filamentous growth growth of unicellular organism as a thread of attached cells invasive filamentous growth 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 transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic 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 sexual reproduction reproductive process conjugation with cellular fusion	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle Rpd3L-Expanded complex protein-containing complex catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle Rpd3L-Expanded complex protein-containing complex catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular membrane-bounded organelle intracellular organelle lumen histone deacetylase complex intracellular organelle nucleoplasm organelle lumen organelle membraneless organelle nuclear lumen Sin3-type complex Rpd3L complex
A	Transcriptional regulatory protein SIN3	transcription coactivator activity transcription regulator activity transcription coregulator 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 cellular component biogenesis positive regulation of metabolic process cellular component assembly 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 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 cellular component biogenesis positive regulation of metabolic process cellular component assembly 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 negative regulation of metabolic process heterochromatin organization 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 positive regulation of biological process negative regulation of chromatin 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 epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of silent mating-type cassette heterochromatin formation negative regulation of biosynthetic process positive regulation of gene expression regulation of heterochromatin organization cellular process negative regulation of heterochromatin organization 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 response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus 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-containing complex organization protein-DNA complex assembly protein-DNA complex organization protein-containing complex assembly nucleosome assembly nucleosome organization RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription 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 sexual reproduction reproductive process meiotic cell cycle cell cycle cell cycle G2/M phase transition mitotic cell cycle process G2/M transition of mitotic cell cycle cell cycle phase transition mitotic cell cycle cell cycle process mitotic cell cycle phase transition 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 negative regulation of transcription by RNA polymerase I transcription by RNA polymerase I regulation of transcription by RNA polymerase I double-strand break repair double-strand break repair via nonhomologous end joining DNA damage response DNA repair	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex Sin3-type complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular membrane-bounded organelle intracellular organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex Sin3-type complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular membrane-bounded organelle intracellular organelle lumen histone deacetylase complex intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle nuclear lumen Rpd3L-Expanded complex Rpd3S complex Rpd3L complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I	IPR001965	Zinc finger, PHD-type	Domain
I	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
I	IPR028651	ING family	Family
I	IPR019787	Zinc finger, PHD-finger	Domain
I	IPR024610	Inhibitor of growth protein, N-terminal histone-binding	Domain
I	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
I	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
H, Q, U, W	IPR009072	Histone-fold	Homologous Superfamily
H, Q, U, W	IPR000164	Histone H3/CENP-A	Family
H, Q, U, W	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
G	IPR038291	SAP30, C-terminal domain superfamily	Homologous Superfamily
G	IPR025718	Histone deacetylase complex subunit SAP30, Sin3 binding domain	Domain
G	IPR024145	Histone deacetylase complex subunit SAP30/SAP30-like	Family
F	IPR013907	Sds3-like	Family
E	IPR013907	Sds3-like	Family
D, N, P, T	IPR009072	Histone-fold	Homologous Superfamily
D, N, P, T	IPR055333	Histone H2B, conserved site	Conserved Site
D, N, P, T	IPR000558	Histone H2B	Family
D, N, P, T	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
C	IPR023801	Histone deacetylase domain	Domain
C	IPR000286	Histone deacetylase HDAC	Family
C	IPR037138	Histone deacetylase domain superfamily	Homologous Superfamily
C	IPR003084	Class I/II Histone deacetylase HDAC	Family
C	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily
B, M, O, S	IPR009072	Histone-fold	Homologous Superfamily
B, M, O, S	IPR002119	Histone H2A	Family
B, M, O, S	IPR032454	Histone H2A, C-terminal domain	Domain
B, M, O, S	IPR032458	Histone H2A conserved site	Conserved Site
B, M, O, S	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
L, R, V, X [auth Z]	IPR009072	Histone-fold	Homologous Superfamily
L, R, V, X [auth Z]	IPR001951	Histone H4	Family
L, R, V, X [auth Z]	IPR035425	CENP-T/Histone H4, histone fold	Domain
L, R, V, X [auth Z]	IPR019809	Histone H4, conserved site	Conserved Site
L, R, V, X [auth Z]	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
K	IPR001965	Zinc finger, PHD-type	Domain
K	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
K	IPR019787	Zinc finger, PHD-finger	Domain
K	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
K	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
K	IPR053051	Histone deacetylase complex subunit	Family
J	IPR039602	Transcriptional regulatory protein Rxt2	Family
J	IPR013904	Transcriptional regulatory protein RXT2, N-terminal	Domain
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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

9V2W | pdb_00009v2w

Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with di-nucleosome

External Resource: Annotation

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage