Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

8IHN

Cryo-EM structure of the Rpd3S core complex

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000786	cellular_component	nucleosome
A	0003677	molecular_function	DNA binding
A	0030527	molecular_function	structural constituent of chromatin
K	0000086	biological_process	G2/M transition of mitotic cell cycle
K	0000122	biological_process	negative regulation of transcription by RNA polymerase II
K	0000785	cellular_component	chromatin
K	0003713	molecular_function	transcription coactivator activity
K	0003714	molecular_function	transcription corepressor activity
K	0005515	molecular_function	protein binding
K	0005634	cellular_component	nucleus
K	0006303	biological_process	double-strand break repair via nonhomologous end joining
K	0006325	biological_process	chromatin organization
K	0006334	biological_process	nucleosome assembly
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	0030174	biological_process	regulation of DNA-templated DNA replication initiation
K	0032221	cellular_component	Rpd3S complex
K	0033698	cellular_component	Rpd3L complex
K	0034605	biological_process	cellular response to heat
K	0042802	molecular_function	identical protein binding
K	0044804	biological_process	nucleophagy
K	0045944	biological_process	positive regulation of transcription by RNA polymerase II
K	0051301	biological_process	cell division
K	0051321	biological_process	meiotic cell cycle
K	0061186	biological_process	negative regulation of silent mating-type cassette heterochromatin formation
K	0061188	biological_process	negative regulation of rDNA heterochromatin formation
K	0070210	cellular_component	Rpd3L-Expanded complex
K	0070550	biological_process	rDNA chromatin condensation
K	0070822	cellular_component	Sin3-type complex
L	0000082	biological_process	G1/S transition of mitotic cell cycle
L	0000086	biological_process	G2/M transition of mitotic cell cycle
L	0000118	cellular_component	histone deacetylase complex
L	0000122	biological_process	negative regulation of transcription by RNA polymerase II
L	0003713	molecular_function	transcription coactivator activity
L	0003714	molecular_function	transcription corepressor activity
L	0004407	molecular_function	histone deacetylase activity
L	0005515	molecular_function	protein binding
L	0005634	cellular_component	nucleus
L	0005737	cellular_component	cytoplasm
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	0006368	biological_process	transcription elongation by RNA polymerase II
L	0006979	biological_process	response to oxidative stress
L	0006995	biological_process	cellular response to nitrogen starvation
L	0008270	molecular_function	zinc ion binding
L	0016239	biological_process	positive regulation of macroautophagy
L	0016479	biological_process	negative regulation of transcription by RNA polymerase I
L	0016787	molecular_function	hydrolase activity
L	0030174	biological_process	regulation of DNA-templated DNA replication initiation
L	0031507	biological_process	heterochromatin formation
L	0032221	cellular_component	Rpd3S complex
L	0033698	cellular_component	Rpd3L complex
L	0034399	cellular_component	nuclear periphery
L	0034503	biological_process	protein localization to nucleolar rDNA repeats
L	0034605	biological_process	cellular response to heat
L	0044804	biological_process	nucleophagy
L	0045128	biological_process	negative regulation of reciprocal meiotic recombination
L	0045944	biological_process	positive regulation of transcription by RNA polymerase II
L	0051321	biological_process	meiotic cell cycle
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	0070211	cellular_component	Snt2C complex
L	0070550	biological_process	rDNA chromatin condensation
L	0070822	cellular_component	Sin3-type complex
M	0000118	cellular_component	histone deacetylase complex
M	0000122	biological_process	negative regulation of transcription by RNA polymerase II
M	0005634	cellular_component	nucleus
M	0006325	biological_process	chromatin organization
M	0006334	biological_process	nucleosome assembly
M	0006357	biological_process	regulation of transcription by RNA polymerase II
M	0006368	biological_process	transcription elongation by RNA polymerase II
M	0008270	molecular_function	zinc ion binding
M	0030174	biological_process	regulation of DNA-templated DNA replication initiation
M	0032221	cellular_component	Rpd3S complex
M	0045944	biological_process	positive regulation of transcription by RNA polymerase II
M	0046872	molecular_function	metal ion binding
M	0060195	biological_process	negative regulation of antisense RNA transcription
N	0000122	biological_process	negative regulation of transcription by RNA polymerase II
N	0000123	cellular_component	histone acetyltransferase complex
N	0005515	molecular_function	protein binding
N	0005634	cellular_component	nucleus
N	0006281	biological_process	DNA repair
N	0006325	biological_process	chromatin organization
N	0006334	biological_process	nucleosome assembly
N	0006335	biological_process	DNA replication-dependent chromatin assembly
N	0006337	biological_process	nucleosome disassembly
N	0006338	biological_process	chromatin remodeling
N	0006351	biological_process	DNA-templated transcription
N	0006355	biological_process	regulation of DNA-templated transcription
N	0006357	biological_process	regulation of transcription by RNA polymerase II
N	0006368	biological_process	transcription elongation by RNA polymerase II
N	0009889	biological_process	regulation of biosynthetic process
N	0030174	biological_process	regulation of DNA-templated DNA replication initiation
N	0032221	cellular_component	Rpd3S complex
N	0032968	biological_process	positive regulation of transcription elongation by RNA polymerase II
N	0035064	molecular_function	methylated histone binding
N	0035267	cellular_component	NuA4 histone acetyltransferase complex
N	0043487	biological_process	regulation of RNA stability
N	0045892	biological_process	negative regulation of DNA-templated transcription
N	0060195	biological_process	negative regulation of antisense RNA transcription
N	1990453	cellular_component	nucleosome disassembly/reassembly complex
O	0000118	cellular_component	histone deacetylase complex
O	0000122	biological_process	negative regulation of transcription by RNA polymerase II
O	0005634	cellular_component	nucleus
O	0006325	biological_process	chromatin organization
O	0006334	biological_process	nucleosome assembly
O	0006357	biological_process	regulation of transcription by RNA polymerase II
O	0006368	biological_process	transcription elongation by RNA polymerase II
O	0008270	molecular_function	zinc ion binding
O	0030174	biological_process	regulation of DNA-templated DNA replication initiation
O	0032221	cellular_component	Rpd3S complex
O	0045944	biological_process	positive regulation of transcription by RNA polymerase II
O	0046872	molecular_function	metal ion binding
O	0060195	biological_process	negative regulation of antisense RNA transcription
P	0000122	biological_process	negative regulation of transcription by RNA polymerase II
P	0000123	cellular_component	histone acetyltransferase complex
P	0005515	molecular_function	protein binding
P	0005634	cellular_component	nucleus
P	0006281	biological_process	DNA repair
P	0006325	biological_process	chromatin organization
P	0006334	biological_process	nucleosome assembly
P	0006335	biological_process	DNA replication-dependent chromatin assembly
P	0006337	biological_process	nucleosome disassembly
P	0006338	biological_process	chromatin remodeling
P	0006351	biological_process	DNA-templated transcription
P	0006355	biological_process	regulation of DNA-templated transcription
P	0006357	biological_process	regulation of transcription by RNA polymerase II
P	0006368	biological_process	transcription elongation by RNA polymerase II
P	0009889	biological_process	regulation of biosynthetic process
P	0030174	biological_process	regulation of DNA-templated DNA replication initiation
P	0032221	cellular_component	Rpd3S complex
P	0032968	biological_process	positive regulation of transcription elongation by RNA polymerase II
P	0035064	molecular_function	methylated histone binding
P	0035267	cellular_component	NuA4 histone acetyltransferase complex
P	0043487	biological_process	regulation of RNA stability
P	0045892	biological_process	negative regulation of DNA-templated transcription
P	0060195	biological_process	negative regulation of antisense RNA transcription
P	1990453	cellular_component	nucleosome disassembly/reassembly complex

Functional Information from PROSITE/UniProt

site_id	PS00322
Number of Residues	7
Details	HISTONE_H3_1 Histone H3 signature 1. KAPRKQL

Chain	Residue	Details
A	LYS14-LEU20

site_id	PS01359
Number of Residues	44
Details	ZF_PHD_1 Zinc finger PHD-type signature. CsaCnqsgsf.......................................LcCdt..Cpks.FHflCldppidpnnlpkgd...............................WhCneC

Chain	Residue	Details
M	CYS263-CYS306

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:19779198

Chain	Residue	Details
N	SER201
P	SER201

site_id	SWS_FT_FI2
Number of Residues	116
Details	ZN_FING: PHD-type 2; atypical => ECO:0000255\|PROSITE-ProRule:PRU00146

Chain	Residue	Details
M	PHE414-THR472
O	PHE414-THR472

site_id	SWS_FT_FI3
Number of Residues	2
Details	MOD_RES: N-acetylmethionine => ECO:0007744\|PubMed:22814378

Chain	Residue	Details
M	MET1
O	MET1

site_id	SWS_FT_FI4
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:18407956

Chain	Residue	Details
M	SER68
O	SER68

site_id	SWS_FT_FI5
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:18407956, ECO:0007744\|PubMed:19779198

Chain	Residue	Details
M	SER683
O	SER683

site_id	SWS_FT_FI6
Number of Residues	1
Details	MOD_RES: Symmetric dimethylarginine; by PRMT5; alternate => ECO:0000250

Chain	Residue	Details
A	ARG8

site_id	SWS_FT_FI7
Number of Residues	1
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000305\|PubMed:12138181

Chain	Residue	Details
A	LYS9

site_id	SWS_FT_FI8
Number of Residues	1
Details	MOD_RES: Phosphoserine; alternate; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5 => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	SER10

site_id	SWS_FT_FI9
Number of Residues	1
Details	MOD_RES: N6-lactoyllysine; alternate => ECO:0000250\|UniProtKB:P84228

Chain	Residue	Details
A	LYS14

site_id	SWS_FT_FI10
Number of Residues	2
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	LYS18
A	LYS23

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)