8IFG

Cryo-EM structure of the Clr6S (Clr6-HDAC) complex from S. pombe

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 [auth B]	PF12265	Histone-binding protein RBBP4 or subunit C of CAF1 complex (CAF1C_H4-bd)	Histone-binding protein RBBP4 or subunit C of CAF1 complex	-	Repeat
A [auth B]	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat
B [auth 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
B [auth A]	PF02671	Paired amphipathic helix repeat (PAH)	Paired amphipathic helix repeat	-	Repeat
B [auth A]	PF16879	C-terminal domain of Sin3a protein (Sin3a_C)	C-terminal domain of Sin3a protein	-	Family
C	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
G [auth P]	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 [auth B]	RbAp48-related WD40 repeat-containing protein prw1	protein binding binding histone binding H3-H4 histone complex chaperone activity protein carrier chaperone histone chaperone activity molecular carrier activity	regulation of cellular process cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process regulation of cellular process cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process transcription initiation at RNA polymerase II promoter regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression cellular metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of DNA-templated transcription	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 chromatin intracellular membrane-bounded organelle cellular anatomical entity organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen cytoplasm cytosol Rpd3L-Expanded complex Rpd3L complex
B [auth A]	Paired amphipathic helix protein pst2	transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity	regulation of cellular process cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process regulation of cellular process cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process transcription initiation at RNA polymerase II promoter regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression cellular metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA 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 transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process	intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle chromatin chromosome cellular anatomical entity non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle protein-containing complex Sin3-type complex membrane-enclosed lumen intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle chromatin chromosome cellular anatomical entity non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle protein-containing complex Sin3-type complex membrane-enclosed lumen nuclear chromosome nuclear protein-containing complex Rpd3S complex intracellular organelle lumen histone deacetylase complex nucleoplasm catalytic complex organelle lumen nuclear lumen
C	Histone deacetylase clr6	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 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds histone deacetylase activity histone H3K9 deacetylase activity histone H3K deacetylase activity histone modifying activity catalytic activity histone H3K14 deacetylase activity histone H4K deacetylase activity histone H4K16 deacetylase activity	regulation of cellular process cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process regulation of cellular process cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process transcription initiation at RNA polymerase II promoter regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression cellular metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process heterochromatin formation negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic	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 chromatin intracellular membrane-bounded organelle cellular anatomical entity organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen cytoplasm cytosol Rpd3L-Expanded complex Rpd3L complex
D [auth E], E [auth D]	Chromatin modification-related protein eaf3	-	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process transcription initiation at RNA polymerase II promoter regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression cellular metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of DNA-templated transcription DNA metabolic process DNA repair DNA repair-dependent chromatin remodeling	protein-containing complex intracellular anatomical structure catalytic complex NuA4 histone acetyltransferase complex chromatin chromosome transferase complex cellular anatomical entity H4/H2A histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex H4 histone acetyltransferase complex intracellular organelle organelle protein-containing complex intracellular anatomical structure catalytic complex NuA4 histone acetyltransferase complex chromatin chromosome transferase complex cellular anatomical entity H4/H2A histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex H4 histone acetyltransferase complex intracellular organelle organelle intracellular non-membrane-bounded organelle protein acetyltransferase complex intracellular protein-containing complex non-membrane-bounded organelle 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
F	Cph1	cation binding ion binding binding metal ion binding small molecule binding	regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process 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 regulation of biosynthetic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process 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 regulation of biosynthetic process regulation of biological process cellular 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 regulation of cellular biosynthetic process regulation of gene expression biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization positive regulation of metabolic process positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process transcription initiation at RNA polymerase II promoter epigenetic regulation of gene expression DNA-templated transcription initiation positive regulation of gene expression transcription initiation-coupled chromatin remodeling positive regulation of cellular biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle protein-containing complex Sin3-type complex membrane-enclosed lumen nuclear chromosome nuclear protein-containing complex intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle protein-containing complex Sin3-type complex membrane-enclosed lumen nuclear chromosome nuclear protein-containing complex Rpd3S complex chromosome intracellular organelle lumen histone deacetylase complex nucleoplasm non-membrane-bounded organelle catalytic complex chromatin organelle lumen intracellular non-membrane-bounded organelle nuclear lumen
G [auth P]	Cph2	cation binding ion binding binding metal ion binding small molecule binding	regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process 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 regulation of biosynthetic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process 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 regulation of biosynthetic process regulation of biological process cellular 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 regulation of cellular biosynthetic process regulation of gene expression biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization positive regulation of metabolic process positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process transcription initiation at RNA polymerase II promoter epigenetic regulation of gene expression DNA-templated transcription initiation positive regulation of gene expression transcription initiation-coupled chromatin remodeling positive regulation of cellular biosynthetic process	intracellular organelle intracellular anatomical structure mitotic spindle cytoskeleton spindle organelle intracellular non-membrane-bounded organelle cellular anatomical entity microtubule cytoskeleton non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle protein-containing complex intracellular organelle intracellular anatomical structure mitotic spindle cytoskeleton spindle organelle intracellular non-membrane-bounded organelle cellular anatomical entity microtubule cytoskeleton non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle protein-containing complex Sin3-type complex membrane-enclosed lumen nuclear chromosome nuclear protein-containing complex Rpd3S complex chromosome intracellular organelle lumen histone deacetylase complex nucleoplasm catalytic complex chromatin organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B]	IPR022052	Histone-binding protein RBBP4, N-terminal	Domain
A [auth B]	IPR050459	WD repeat RBAP46/RBAP48/MSI1	Family
A [auth B]	IPR019775	WD40 repeat, conserved site	Conserved Site
A [auth B]	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A [auth B]	IPR001680	WD40 repeat	Repeat
A [auth B]	IPR020472	G-protein beta WD-40 repeat	Repeat
A [auth B]	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
B [auth A]	IPR031693	Sin3, C-terminal	Domain
B [auth A]	IPR013194	Histone deacetylase interacting domain	Domain
B [auth A]	IPR003822	Paired amphipathic helix	Repeat
B [auth A]	IPR036600	Paired amphipathic helix superfamily	Homologous Superfamily
B [auth A]	IPR039774	Transcriptional regulatory protein Sin3-like	Family
C	IPR000286	Histone deacetylase family	Family
C	IPR003084	Histone deacetylase	Family
C	IPR023801	Histone deacetylase domain	Domain
C	IPR037138	Histone deacetylase domain superfamily	Homologous Superfamily
C	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily
C	IPR050284	Histone deacetylase and polyamine deacetylase	Family
D [auth E], E [auth D]	IPR000953	Chromo/chromo shadow domain	Domain
D [auth E], E [auth D]	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
D [auth E], E [auth D]	IPR025995	RNA binding activity-knot of a chromodomain	Domain
D [auth E], E [auth D]	IPR008676	MRG	Family
D [auth E], E [auth D]	IPR026541	MRG domain	Domain
D [auth E], E [auth D]	IPR038217	MRG, C-terminal domain superfamily	Homologous Superfamily
F	IPR001965	Zinc finger, PHD-type	Domain
F	IPR019787	Zinc finger, PHD-finger	Domain
F	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
F	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
F	IPR052819	Chromatin-associated regulatory protein	Family
F	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
G [auth P]	IPR001965	Zinc finger, PHD-type	Domain
G [auth P]	IPR019787	Zinc finger, PHD-finger	Domain
G [auth P]	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
G [auth P]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
G [auth P]	IPR052819	Chromatin-associated regulatory protein	Family
G [auth P]	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site

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.

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8IFG

Cryo-EM structure of the Clr6S (Clr6-HDAC) complex from S. pombe

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