Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

8HXX

Cryo-EM structure of the histone deacetylase complex Rpd3S

Functional Information from GO Data

Chain	GOid	namespace	contents
E	0000786	cellular_component	nucleosome
E	0003677	molecular_function	DNA binding
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005694	cellular_component	chromosome
E	0030527	molecular_function	structural constituent of chromatin
E	0046982	molecular_function	protein heterodimerization activity
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	0000122	biological_process	negative regulation of transcription by RNA polymerase II
M	0000123	cellular_component	histone acetyltransferase complex
M	0005515	molecular_function	protein binding
M	0005634	cellular_component	nucleus
M	0006281	biological_process	DNA repair
M	0006325	biological_process	chromatin organization
M	0006334	biological_process	nucleosome assembly
M	0006335	biological_process	DNA replication-dependent chromatin assembly
M	0006337	biological_process	nucleosome disassembly
M	0006338	biological_process	chromatin remodeling
M	0006351	biological_process	DNA-templated transcription
M	0006355	biological_process	regulation of DNA-templated transcription
M	0006357	biological_process	regulation of transcription by RNA polymerase II
M	0006368	biological_process	transcription elongation by RNA polymerase II
M	0009889	biological_process	regulation of biosynthetic process
M	0030174	biological_process	regulation of DNA-templated DNA replication initiation
M	0032221	cellular_component	Rpd3S complex
M	0032968	biological_process	positive regulation of transcription elongation by RNA polymerase II
M	0035064	molecular_function	methylated histone binding
M	0035267	cellular_component	NuA4 histone acetyltransferase complex
M	0043487	biological_process	regulation of RNA stability
M	0045892	biological_process	negative regulation of DNA-templated transcription
M	0060195	biological_process	negative regulation of antisense RNA transcription
M	1990453	cellular_component	nucleosome disassembly/reassembly complex
N	0000118	cellular_component	histone deacetylase complex
N	0000122	biological_process	negative regulation of transcription by RNA polymerase II
N	0005634	cellular_component	nucleus
N	0006325	biological_process	chromatin organization
N	0006334	biological_process	nucleosome assembly
N	0006357	biological_process	regulation of transcription by RNA polymerase II
N	0006368	biological_process	transcription elongation by RNA polymerase II
N	0008270	molecular_function	zinc ion binding
N	0030174	biological_process	regulation of DNA-templated DNA replication initiation
N	0032221	cellular_component	Rpd3S complex
N	0045944	biological_process	positive regulation of transcription by RNA polymerase II
N	0046872	molecular_function	metal ion binding
N	0060195	biological_process	negative regulation of antisense RNA transcription
O	0000122	biological_process	negative regulation of transcription by RNA polymerase II
O	0000123	cellular_component	histone acetyltransferase complex
O	0005515	molecular_function	protein binding
O	0005634	cellular_component	nucleus
O	0006281	biological_process	DNA repair
O	0006325	biological_process	chromatin organization
O	0006334	biological_process	nucleosome assembly
O	0006335	biological_process	DNA replication-dependent chromatin assembly
O	0006337	biological_process	nucleosome disassembly
O	0006338	biological_process	chromatin remodeling
O	0006351	biological_process	DNA-templated transcription
O	0006355	biological_process	regulation of DNA-templated transcription
O	0006357	biological_process	regulation of transcription by RNA polymerase II
O	0006368	biological_process	transcription elongation by RNA polymerase II
O	0009889	biological_process	regulation of biosynthetic process
O	0030174	biological_process	regulation of DNA-templated DNA replication initiation
O	0032221	cellular_component	Rpd3S complex
O	0032968	biological_process	positive regulation of transcription elongation by RNA polymerase II
O	0035064	molecular_function	methylated histone binding
O	0035267	cellular_component	NuA4 histone acetyltransferase complex
O	0043487	biological_process	regulation of RNA stability
O	0045892	biological_process	negative regulation of DNA-templated transcription
O	0060195	biological_process	negative regulation of antisense RNA transcription
O	1990453	cellular_component	nucleosome disassembly/reassembly complex
P	0000118	cellular_component	histone deacetylase complex
P	0000122	biological_process	negative regulation of transcription by RNA polymerase II
P	0005634	cellular_component	nucleus
P	0006325	biological_process	chromatin organization
P	0006334	biological_process	nucleosome assembly
P	0006357	biological_process	regulation of transcription by RNA polymerase II
P	0006368	biological_process	transcription elongation by RNA polymerase II
P	0008270	molecular_function	zinc ion binding
P	0030174	biological_process	regulation of DNA-templated DNA replication initiation
P	0032221	cellular_component	Rpd3S complex
P	0045944	biological_process	positive regulation of transcription by RNA polymerase II
P	0046872	molecular_function	metal ion binding
P	0060195	biological_process	negative regulation of antisense RNA transcription

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
E	LYS14-LEU20

site_id	PS00959
Number of Residues	9
Details	HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI

Chain	Residue	Details
E	PRO66-ILE74

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

Chain	Residue	Details
N	CYS263-CYS306

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	98
Details	ZN_FING: PHD-type 1 => ECO:0000255\|PROSITE-ProRule:PRU00146

Chain	Residue	Details
N	GLU260-LYS309
P	GLU260-LYS309

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

Chain	Residue	Details
N	PHE414-THR472
P	PHE414-THR472

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

Chain	Residue	Details
N	MET1
P	MET1

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

Chain	Residue	Details
N	SER68
P	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
N	SER683
P	SER683

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

Chain	Residue	Details
E	ARG8

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

Chain	Residue	Details
E	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
E	SER10

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

Chain	Residue	Details
E	LYS14

site_id	SWS_FT_FI10
Number of Residues	5
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
E	LYS18
E	LYS23
E	LYS27
E	ML336
E	LYS64

site_id	SWS_FT_FI11
Number of Residues	1
Details	MOD_RES: Citrulline => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
E	ARG26

site_id	SWS_FT_FI12
Number of Residues	1
Details	MOD_RES: Phosphoserine; alternate; by AURKB, AURKC and RPS6KA5 => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
E	SER28

site_id	SWS_FT_FI13
Number of Residues	1
Details	MOD_RES: N6-methyllysine => ECO:0000250\|UniProtKB:P68431

Chain	Residue	Details
E	LYS37

site_id	SWS_FT_FI14
Number of Residues	1
Details	MOD_RES: Phosphotyrosine => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
E	TYR41

site_id	SWS_FT_FI15
Number of Residues	2
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000250\|UniProtKB:P84228

Chain	Residue	Details
E	LYS56
E	LYS79

site_id	SWS_FT_FI16
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
E	SER57

site_id	SWS_FT_FI17
Number of Residues	2
Details	MOD_RES: Phosphothreonine => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
E	THR80
E	THR107

site_id	SWS_FT_FI18
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0000250\|UniProtKB:P84243

Chain	Residue	Details
E	SER86

site_id	SWS_FT_FI19
Number of Residues	1
Details	MOD_RES: N6-glutaryllysine; alternate => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
E	LYS115

site_id	SWS_FT_FI20
Number of Residues	1
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
E	LYS122

site_id	SWS_FT_FI21
Number of Residues	1
Details	LIPID: S-palmitoyl cysteine => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
E	ALA110

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