8GA8

Structure of the yeast (HDAC) Rpd3L complex

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	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	0000082	biological_process	G1/S transition of mitotic cell cycle
B	0000086	biological_process	G2/M transition of mitotic cell cycle
B	0000118	cellular_component	histone deacetylase complex
B	0000122	biological_process	negative regulation of transcription by RNA polymerase II
B	0003713	molecular_function	transcription coactivator activity
B	0003714	molecular_function	transcription corepressor activity
B	0004407	molecular_function	histone deacetylase activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
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	0006368	biological_process	transcription elongation by RNA polymerase II
B	0006979	biological_process	response to oxidative stress
B	0006995	biological_process	cellular response to nitrogen starvation
B	0008270	molecular_function	zinc ion binding
B	0016239	biological_process	positive regulation of macroautophagy
B	0016479	biological_process	negative regulation of transcription by RNA polymerase I
B	0016787	molecular_function	hydrolase activity
B	0030174	biological_process	regulation of DNA-templated DNA replication initiation
B	0031507	biological_process	heterochromatin formation
B	0032221	cellular_component	Rpd3S complex
B	0033698	cellular_component	Rpd3L complex
B	0034399	cellular_component	nuclear periphery
B	0034503	biological_process	protein localization to nucleolar rDNA repeats
B	0034605	biological_process	cellular response to heat
B	0044804	biological_process	nucleophagy
B	0045128	biological_process	negative regulation of reciprocal meiotic recombination
B	0045944	biological_process	positive regulation of transcription by RNA polymerase II
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	0070211	cellular_component	Snt2C complex
B	0070550	biological_process	rDNA chromatin condensation
B	0070822	cellular_component	Sin3-type complex
D	0000086	biological_process	G2/M transition of mitotic cell cycle
D	0000122	biological_process	negative regulation of transcription by RNA polymerase II
D	0000785	cellular_component	chromatin
D	0003713	molecular_function	transcription coactivator activity
D	0003714	molecular_function	transcription corepressor activity
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0006303	biological_process	double-strand break repair via nonhomologous end joining
D	0006325	biological_process	chromatin organization
D	0006334	biological_process	nucleosome assembly
D	0006355	biological_process	regulation of DNA-templated transcription
D	0006357	biological_process	regulation of transcription by RNA polymerase II
D	0016479	biological_process	negative regulation of transcription by RNA polymerase I
D	0030174	biological_process	regulation of DNA-templated DNA replication initiation
D	0032221	cellular_component	Rpd3S complex
D	0033698	cellular_component	Rpd3L complex
D	0034605	biological_process	cellular response to heat
D	0042802	molecular_function	identical protein binding
D	0044804	biological_process	nucleophagy
D	0045944	biological_process	positive regulation of transcription by RNA polymerase II
D	0051301	biological_process	cell division
D	0051321	biological_process	meiotic cell cycle
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	0070550	biological_process	rDNA chromatin condensation
D	0070822	cellular_component	Sin3-type complex
E	0000082	biological_process	G1/S transition of mitotic cell cycle
E	0000086	biological_process	G2/M transition of mitotic cell cycle
E	0000118	cellular_component	histone deacetylase complex
E	0000122	biological_process	negative regulation of transcription by RNA polymerase II
E	0003713	molecular_function	transcription coactivator activity
E	0003714	molecular_function	transcription corepressor activity
E	0004407	molecular_function	histone deacetylase activity
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005737	cellular_component	cytoplasm
E	0006325	biological_process	chromatin organization
E	0006334	biological_process	nucleosome assembly
E	0006355	biological_process	regulation of DNA-templated transcription
E	0006357	biological_process	regulation of transcription by RNA polymerase II
E	0006368	biological_process	transcription elongation by RNA polymerase II
E	0006979	biological_process	response to oxidative stress
E	0006995	biological_process	cellular response to nitrogen starvation
E	0008270	molecular_function	zinc ion binding
E	0016239	biological_process	positive regulation of macroautophagy
E	0016479	biological_process	negative regulation of transcription by RNA polymerase I
E	0016787	molecular_function	hydrolase activity
E	0030174	biological_process	regulation of DNA-templated DNA replication initiation
E	0031507	biological_process	heterochromatin formation
E	0032221	cellular_component	Rpd3S complex
E	0033698	cellular_component	Rpd3L complex
E	0034399	cellular_component	nuclear periphery
E	0034503	biological_process	protein localization to nucleolar rDNA repeats
E	0034605	biological_process	cellular response to heat
E	0044804	biological_process	nucleophagy
E	0045128	biological_process	negative regulation of reciprocal meiotic recombination
E	0045944	biological_process	positive regulation of transcription by RNA polymerase II
E	0051321	biological_process	meiotic cell cycle
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	0070211	cellular_component	Snt2C complex
E	0070550	biological_process	rDNA chromatin condensation
E	0070822	cellular_component	Sin3-type complex
G	0000122	biological_process	negative regulation of transcription by RNA polymerase II
G	0003674	molecular_function	molecular_function
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005654	cellular_component	nucleoplasm
G	0005737	cellular_component	cytoplasm
G	0005739	cellular_component	mitochondrion
G	0006325	biological_process	chromatin organization
G	0006334	biological_process	nucleosome assembly
G	0006357	biological_process	regulation of transcription by RNA polymerase II
G	0010468	biological_process	regulation of gene expression
G	0030174	biological_process	regulation of DNA-templated DNA replication initiation
G	0033698	cellular_component	Rpd3L complex
G	0034605	biological_process	cellular response to heat
G	0042826	molecular_function	histone deacetylase binding
G	0045944	biological_process	positive regulation of transcription by RNA polymerase II
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	0070822	cellular_component	Sin3-type complex
G	1900089	biological_process	negative regulation of inositol biosynthetic process
G	1900090	biological_process	positive regulation of inositol biosynthetic process
G	1900469	biological_process	negative regulation of phosphatidylserine biosynthetic process
G	1900470	biological_process	positive regulation of phosphatidylserine biosynthetic process
G	2001246	biological_process	negative regulation of phosphatidylcholine biosynthetic process
G	2001247	biological_process	positive regulation of phosphatidylcholine biosynthetic process
H	0000122	biological_process	negative regulation of transcription by RNA polymerase II
H	0004407	molecular_function	histone deacetylase activity
H	0005634	cellular_component	nucleus
H	0005654	cellular_component	nucleoplasm
H	0005829	cellular_component	cytosol
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	0031507	biological_process	heterochromatin formation
H	0033698	cellular_component	Rpd3L complex
H	0034605	biological_process	cellular response to heat
H	0042826	molecular_function	histone deacetylase binding
H	0043709	biological_process	cell adhesion involved in single-species biofilm formation
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	2000217	biological_process	regulation of invasive growth in response to glucose limitation
J	0000118	cellular_component	histone deacetylase complex
J	0003712	molecular_function	transcription coregulator activity
J	0003714	molecular_function	transcription corepressor activity
J	0005634	cellular_component	nucleus
J	0006325	biological_process	chromatin organization
J	0006334	biological_process	nucleosome assembly
J	0006355	biological_process	regulation of DNA-templated transcription
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	0034605	biological_process	cellular response to heat
J	0045944	biological_process	positive regulation of transcription by RNA polymerase II
J	0061186	biological_process	negative regulation of silent mating-type cassette heterochromatin formation
J	0061188	biological_process	negative regulation of rDNA heterochromatin formation
J	0070210	cellular_component	Rpd3L-Expanded complex
J	2000219	biological_process	positive regulation of invasive growth in response to glucose limitation
K	0003674	molecular_function	molecular_function
K	0005634	cellular_component	nucleus
K	0006325	biological_process	chromatin organization
K	0006334	biological_process	nucleosome assembly
K	0006357	biological_process	regulation of transcription by RNA polymerase II
K	0016479	biological_process	negative regulation of transcription by RNA polymerase I
K	0033698	cellular_component	Rpd3L complex
K	0070210	cellular_component	Rpd3L-Expanded complex
L	0000118	cellular_component	histone deacetylase complex
L	0000785	cellular_component	chromatin
L	0005634	cellular_component	nucleus
L	0006325	biological_process	chromatin organization
L	0006334	biological_process	nucleosome assembly
L	0006355	biological_process	regulation of DNA-templated transcription
L	0006357	biological_process	regulation of transcription by RNA polymerase II
L	0008270	molecular_function	zinc ion binding
L	0016479	biological_process	negative regulation of transcription by RNA polymerase I
L	0033698	cellular_component	Rpd3L complex
L	0034605	biological_process	cellular response to heat
L	0035064	molecular_function	methylated histone binding
L	0045944	biological_process	positive regulation of transcription by RNA polymerase II
L	0046872	molecular_function	metal ion binding
L	0061186	biological_process	negative regulation of silent mating-type cassette heterochromatin formation
L	0061188	biological_process	negative regulation of rDNA heterochromatin formation
L	0070210	cellular_component	Rpd3L-Expanded complex
L	2000219	biological_process	positive regulation of invasive growth in response to glucose limitation
M	0000122	biological_process	negative regulation of transcription by RNA polymerase II
M	0000747	biological_process	conjugation with cellular fusion
M	0001403	biological_process	invasive growth in response to glucose limitation
M	0004407	molecular_function	histone deacetylase activity
M	0005515	molecular_function	protein binding
M	0005634	cellular_component	nucleus
M	0005829	cellular_component	cytosol
M	0006325	biological_process	chromatin organization
M	0006334	biological_process	nucleosome assembly
M	0006357	biological_process	regulation of transcription by RNA polymerase II
M	0033698	cellular_component	Rpd3L complex
M	0061186	biological_process	negative regulation of silent mating-type cassette heterochromatin formation
M	0061188	biological_process	negative regulation of rDNA heterochromatin formation
M	0070210	cellular_component	Rpd3L-Expanded complex
M	2000219	biological_process	positive regulation of invasive growth in response to glucose limitation

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
L	CYS283-CYS326

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Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	MOD_RES: N-acetylserine => ECO:0007744|PubMed:22814378

Chain	Residue	Details
K	SER2
E	HIS151

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site_id	SWS_FT_FI2
Number of Residues	2
Details	MOD_RES: Phosphothreonine => ECO:0007744|PubMed:17330950, ECO:0007744|PubMed:18407956

Chain	Residue	Details
B	THR394
E	THR394
L	CYS296
L	CYS301
L	HIS307
L	CYS310
L	CYS323
L	CYS326

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site_id	SWS_FT_FI3
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198

Chain	Residue	Details
B	SER408
E	SER408
L	ASP297
L	TRP305

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site_id	SWS_FT_FI4
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:19779198

Chain	Residue	Details
A	SER316
A	SER1046
D	SER316
D	SER1046

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