8HPO

Cryo-EM structure of a SIN3/HDAC complex from budding yeast

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000086	biological_process	G2/M transition of mitotic cell cycle
A	0000122	biological_process	negative regulation of transcription by RNA polymerase II
A	0000785	cellular_component	chromatin
A	0003713	molecular_function	transcription coactivator activity
A	0003714	molecular_function	transcription corepressor activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0006303	biological_process	double-strand break repair via nonhomologous end joining
A	0006325	biological_process	chromatin organization
A	0006334	biological_process	nucleosome assembly
A	0006355	biological_process	regulation of DNA-templated transcription
A	0006357	biological_process	regulation of transcription by RNA polymerase II
A	0010558	biological_process	negative regulation of macromolecule biosynthetic process
A	0010628	biological_process	positive regulation of gene expression
A	0016479	biological_process	negative regulation of transcription by RNA polymerase I
A	0030174	biological_process	regulation of DNA-templated DNA replication initiation
A	0032221	cellular_component	Rpd3S complex
A	0033698	cellular_component	Rpd3L complex
A	0034605	biological_process	cellular response to heat
A	0042802	molecular_function	identical protein binding
A	0044804	biological_process	nucleophagy
A	0045944	biological_process	positive regulation of transcription by RNA polymerase II
A	0051301	biological_process	cell division
A	0051321	biological_process	meiotic cell cycle
A	0061186	biological_process	negative regulation of silent mating-type cassette heterochromatin formation
A	0061188	biological_process	negative regulation of rDNA heterochromatin formation
A	0070210	cellular_component	Rpd3L-Expanded complex
A	0070550	biological_process	rDNA chromatin condensation
A	0070822	cellular_component	Sin3-type complex
B	0000086	biological_process	G2/M transition of mitotic cell cycle
B	0000122	biological_process	negative regulation of transcription by RNA polymerase II
B	0000785	cellular_component	chromatin
B	0003713	molecular_function	transcription coactivator activity
B	0003714	molecular_function	transcription corepressor activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0006303	biological_process	double-strand break repair via nonhomologous end joining
B	0006325	biological_process	chromatin organization
B	0006334	biological_process	nucleosome assembly
B	0006355	biological_process	regulation of DNA-templated transcription
B	0006357	biological_process	regulation of transcription by RNA polymerase II
B	0010558	biological_process	negative regulation of macromolecule biosynthetic process
B	0010628	biological_process	positive regulation of gene expression
B	0016479	biological_process	negative regulation of transcription by RNA polymerase I
B	0030174	biological_process	regulation of DNA-templated DNA replication initiation
B	0032221	cellular_component	Rpd3S complex
B	0033698	cellular_component	Rpd3L complex
B	0034605	biological_process	cellular response to heat
B	0042802	molecular_function	identical protein binding
B	0044804	biological_process	nucleophagy
B	0045944	biological_process	positive regulation of transcription by RNA polymerase II
B	0051301	biological_process	cell division
B	0051321	biological_process	meiotic cell cycle
B	0061186	biological_process	negative regulation of silent mating-type cassette heterochromatin formation
B	0061188	biological_process	negative regulation of rDNA heterochromatin formation
B	0070210	cellular_component	Rpd3L-Expanded complex
B	0070550	biological_process	rDNA chromatin condensation
B	0070822	cellular_component	Sin3-type complex
C	0000118	cellular_component	histone deacetylase complex
C	0000785	cellular_component	chromatin
C	0005634	cellular_component	nucleus
C	0006325	biological_process	chromatin organization
C	0006334	biological_process	nucleosome assembly
C	0006355	biological_process	regulation of DNA-templated transcription
C	0006357	biological_process	regulation of transcription by RNA polymerase II
C	0008270	molecular_function	zinc ion binding
C	0016479	biological_process	negative regulation of transcription by RNA polymerase I
C	0033698	cellular_component	Rpd3L complex
C	0034605	biological_process	cellular response to heat
C	0045944	biological_process	positive regulation of transcription by RNA polymerase II
C	0046872	molecular_function	metal ion binding
C	0061186	biological_process	negative regulation of silent mating-type cassette heterochromatin formation
C	0061188	biological_process	negative regulation of rDNA heterochromatin formation
C	0070210	cellular_component	Rpd3L-Expanded complex
C	0140002	molecular_function	histone H3K4me3 reader activity
C	2000219	biological_process	positive regulation of invasive growth in response to glucose limitation
D	0000122	biological_process	negative regulation of transcription by RNA polymerase II
D	0004407	molecular_function	histone deacetylase activity
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005829	cellular_component	cytosol
D	0006325	biological_process	chromatin organization
D	0006334	biological_process	nucleosome assembly
D	0006357	biological_process	regulation of transcription by RNA polymerase II
D	0010468	biological_process	regulation of gene expression
D	0031507	biological_process	heterochromatin formation
D	0033698	cellular_component	Rpd3L complex
D	0034605	biological_process	cellular response to heat
D	0042826	molecular_function	histone deacetylase binding
D	0043709	biological_process	cell adhesion involved in single-species biofilm formation
D	0045944	biological_process	positive regulation of transcription by RNA polymerase II
D	0061186	biological_process	negative regulation of silent mating-type cassette heterochromatin formation
D	0061188	biological_process	negative regulation of rDNA heterochromatin formation
D	0070210	cellular_component	Rpd3L-Expanded complex
D	0070822	cellular_component	Sin3-type complex
D	2000217	biological_process	regulation of invasive growth in response to glucose limitation
E	0000122	biological_process	negative regulation of transcription by RNA polymerase II
E	0000747	biological_process	conjugation with cellular fusion
E	0001403	biological_process	invasive growth in response to glucose limitation
E	0004407	molecular_function	histone deacetylase activity
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005829	cellular_component	cytosol
E	0006325	biological_process	chromatin organization
E	0006334	biological_process	nucleosome assembly
E	0006357	biological_process	regulation of transcription by RNA polymerase II
E	0033698	cellular_component	Rpd3L complex
E	0061186	biological_process	negative regulation of silent mating-type cassette heterochromatin formation
E	0061188	biological_process	negative regulation of rDNA heterochromatin formation
E	0070210	cellular_component	Rpd3L-Expanded complex
E	2000219	biological_process	positive regulation of invasive growth in response to glucose limitation
F	0000082	biological_process	G1/S transition of mitotic cell cycle
F	0000086	biological_process	G2/M transition of mitotic cell cycle
F	0000118	cellular_component	histone deacetylase complex
F	0000122	biological_process	negative regulation of transcription by RNA polymerase II
F	0003713	molecular_function	transcription coactivator activity
F	0003714	molecular_function	transcription corepressor activity
F	0004407	molecular_function	histone deacetylase activity
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005737	cellular_component	cytoplasm
F	0006325	biological_process	chromatin organization
F	0006334	biological_process	nucleosome assembly
F	0006355	biological_process	regulation of DNA-templated transcription
F	0006357	biological_process	regulation of transcription by RNA polymerase II
F	0006368	biological_process	transcription elongation by RNA polymerase II
F	0006979	biological_process	response to oxidative stress
F	0006995	biological_process	cellular response to nitrogen starvation
F	0008270	molecular_function	zinc ion binding
F	0010557	biological_process	positive regulation of macromolecule biosynthetic process
F	0016239	biological_process	positive regulation of macroautophagy
F	0016479	biological_process	negative regulation of transcription by RNA polymerase I
F	0016787	molecular_function	hydrolase activity
F	0030174	biological_process	regulation of DNA-templated DNA replication initiation
F	0031507	biological_process	heterochromatin formation
F	0032221	cellular_component	Rpd3S complex
F	0033698	cellular_component	Rpd3L complex
F	0034399	cellular_component	nuclear periphery
F	0034503	biological_process	protein localization to nucleolar rDNA repeats
F	0034605	biological_process	cellular response to heat
F	0044804	biological_process	nucleophagy
F	0045128	biological_process	negative regulation of reciprocal meiotic recombination
F	0045944	biological_process	positive regulation of transcription by RNA polymerase II
F	0051321	biological_process	meiotic cell cycle
F	0061186	biological_process	negative regulation of silent mating-type cassette heterochromatin formation
F	0061188	biological_process	negative regulation of rDNA heterochromatin formation
F	0070210	cellular_component	Rpd3L-Expanded complex
F	0070211	cellular_component	Snt2C complex
F	0070550	biological_process	rDNA chromatin condensation
F	0070822	cellular_component	Sin3-type complex
F	0141221	molecular_function	histone deacetylase activity, hydrolytic mechanism
G	0000082	biological_process	G1/S transition of mitotic cell cycle
G	0000086	biological_process	G2/M transition of mitotic cell cycle
G	0000118	cellular_component	histone deacetylase complex
G	0000122	biological_process	negative regulation of transcription by RNA polymerase II
G	0003713	molecular_function	transcription coactivator activity
G	0003714	molecular_function	transcription corepressor activity
G	0004407	molecular_function	histone deacetylase activity
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005737	cellular_component	cytoplasm
G	0006325	biological_process	chromatin organization
G	0006334	biological_process	nucleosome assembly
G	0006355	biological_process	regulation of DNA-templated transcription
G	0006357	biological_process	regulation of transcription by RNA polymerase II
G	0006368	biological_process	transcription elongation by RNA polymerase II
G	0006979	biological_process	response to oxidative stress
G	0006995	biological_process	cellular response to nitrogen starvation
G	0008270	molecular_function	zinc ion binding
G	0010557	biological_process	positive regulation of macromolecule biosynthetic process
G	0016239	biological_process	positive regulation of macroautophagy
G	0016479	biological_process	negative regulation of transcription by RNA polymerase I
G	0016787	molecular_function	hydrolase activity
G	0030174	biological_process	regulation of DNA-templated DNA replication initiation
G	0031507	biological_process	heterochromatin formation
G	0032221	cellular_component	Rpd3S complex
G	0033698	cellular_component	Rpd3L complex
G	0034399	cellular_component	nuclear periphery
G	0034503	biological_process	protein localization to nucleolar rDNA repeats
G	0034605	biological_process	cellular response to heat
G	0044804	biological_process	nucleophagy
G	0045128	biological_process	negative regulation of reciprocal meiotic recombination
G	0045944	biological_process	positive regulation of transcription by RNA polymerase II
G	0051321	biological_process	meiotic cell cycle
G	0061186	biological_process	negative regulation of silent mating-type cassette heterochromatin formation
G	0061188	biological_process	negative regulation of rDNA heterochromatin formation
G	0070210	cellular_component	Rpd3L-Expanded complex
G	0070211	cellular_component	Snt2C complex
G	0070550	biological_process	rDNA chromatin condensation
G	0070822	cellular_component	Sin3-type complex
G	0141221	molecular_function	histone deacetylase activity, hydrolytic mechanism
H	0000122	biological_process	negative regulation of transcription by RNA polymerase II
H	0003674	molecular_function	molecular_function
H	0005515	molecular_function	protein binding
H	0005634	cellular_component	nucleus
H	0005654	cellular_component	nucleoplasm
H	0005737	cellular_component	cytoplasm
H	0005739	cellular_component	mitochondrion
H	0006325	biological_process	chromatin organization
H	0006334	biological_process	nucleosome assembly
H	0006357	biological_process	regulation of transcription by RNA polymerase II
H	0010468	biological_process	regulation of gene expression
H	0030174	biological_process	regulation of DNA-templated DNA replication initiation
H	0033698	cellular_component	Rpd3L complex
H	0034605	biological_process	cellular response to heat
H	0042826	molecular_function	histone deacetylase binding
H	0045944	biological_process	positive regulation of transcription by RNA polymerase II
H	0061186	biological_process	negative regulation of silent mating-type cassette heterochromatin formation
H	0061188	biological_process	negative regulation of rDNA heterochromatin formation
H	0070210	cellular_component	Rpd3L-Expanded complex
H	0070822	cellular_component	Sin3-type complex
H	1900089	biological_process	negative regulation of inositol biosynthetic process
H	1900090	biological_process	positive regulation of inositol biosynthetic process
H	1900469	biological_process	negative regulation of phosphatidylserine biosynthetic process
H	1900470	biological_process	positive regulation of phosphatidylserine biosynthetic process
H	2001246	biological_process	negative regulation of phosphatidylcholine biosynthetic process
H	2001247	biological_process	positive regulation of phosphatidylcholine biosynthetic process
I	0000118	cellular_component	histone deacetylase complex
I	0003712	molecular_function	transcription coregulator activity
I	0003714	molecular_function	transcription corepressor activity
I	0005634	cellular_component	nucleus
I	0006325	biological_process	chromatin organization
I	0006334	biological_process	nucleosome assembly
I	0006355	biological_process	regulation of DNA-templated transcription
I	0006357	biological_process	regulation of transcription by RNA polymerase II
I	0016479	biological_process	negative regulation of transcription by RNA polymerase I
I	0033698	cellular_component	Rpd3L complex
I	0034605	biological_process	cellular response to heat
I	0045944	biological_process	positive regulation of transcription by RNA polymerase II
I	0061186	biological_process	negative regulation of silent mating-type cassette heterochromatin formation
I	0061188	biological_process	negative regulation of rDNA heterochromatin formation
I	0070210	cellular_component	Rpd3L-Expanded complex
I	2000219	biological_process	positive regulation of invasive growth in response to glucose limitation
J	0003674	molecular_function	molecular_function
J	0005634	cellular_component	nucleus
J	0006325	biological_process	chromatin organization
J	0006334	biological_process	nucleosome assembly
J	0006357	biological_process	regulation of transcription by RNA polymerase II
J	0016479	biological_process	negative regulation of transcription by RNA polymerase I
J	0033698	cellular_component	Rpd3L complex
J	0070210	cellular_component	Rpd3L-Expanded complex
K	0000122	biological_process	negative regulation of transcription by RNA polymerase II
K	0003714	molecular_function	transcription corepressor activity
K	0005634	cellular_component	nucleus
K	0005737	cellular_component	cytoplasm
K	0006325	biological_process	chromatin organization
K	0006334	biological_process	nucleosome assembly
K	0006338	biological_process	chromatin remodeling
K	0006355	biological_process	regulation of DNA-templated transcription
K	0006357	biological_process	regulation of transcription by RNA polymerase II
K	0016479	biological_process	negative regulation of transcription by RNA polymerase I
K	0032221	cellular_component	Rpd3S complex
K	0033698	cellular_component	Rpd3L complex
K	0034605	biological_process	cellular response to heat
K	0040020	biological_process	regulation of meiotic nuclear division
K	0042393	molecular_function	histone binding
K	0045944	biological_process	positive regulation of transcription by RNA polymerase II
K	0051321	biological_process	meiotic cell cycle
K	0070210	cellular_component	Rpd3L-Expanded complex

Functional Information from PROSITE/UniProt

site_id	PS01359
Number of Residues	44
Details	ZF_PHD_1 Zinc finger PHD-type signature. Cy.Cnqvaygem.....................................VgCdgadCelewFHlpCigletlpkgk...................................WyCddC

Chain	Residue	Details
C	CYS283-CYS326

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Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	38
Details	Repeat: {"description":"WD 1"}

Chain

Residue

Details

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site_id	SWS_FT_FI2
Number of Residues	40
Details	Repeat: {"description":"WD 2"}

Chain

Residue

Details

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site_id	SWS_FT_FI3
Number of Residues	40
Details	Repeat: {"description":"WD 3"}

Chain

Residue

Details

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site_id	SWS_FT_FI4
Number of Residues	8
Details	Motif: {"description":"NEE-box"}

Chain

Residue

Details

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site_id	SWS_FT_FI5
Number of Residues	74
Details	Coiled coil: {"evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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site_id	SWS_FT_FI6
Number of Residues	40
Details	Motif: {"description":"ESA1-RPD3 motif"}

Chain

Residue

Details

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site_id	SWS_FT_FI7
Number of Residues	2
Details	Active site: {"evidences":[{"evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

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site_id	SWS_FT_FI8
Number of Residues	312
Details	Region: {"description":"Histone deacetylase"}

Chain

Residue

Details

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site_id	SWS_FT_FI9
Number of Residues	71
Details	Domain: {"description":"PAH 3","evidences":[{"source":"PROSITE-ProRule","id":"PRU00810","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

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