Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

8KD4

Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000082	biological_process	G1/S transition of mitotic cell cycle
A	0000086	biological_process	G2/M transition of mitotic cell cycle
A	0000118	cellular_component	histone deacetylase complex
A	0000122	biological_process	negative regulation of transcription by RNA polymerase II
A	0003713	molecular_function	transcription coactivator activity
A	0003714	molecular_function	transcription corepressor activity
A	0004407	molecular_function	histone deacetylase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
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	0006368	biological_process	transcription elongation by RNA polymerase II
A	0006979	biological_process	response to oxidative stress
A	0006995	biological_process	cellular response to nitrogen starvation
A	0008270	molecular_function	zinc ion binding
A	0016239	biological_process	positive regulation of macroautophagy
A	0016479	biological_process	negative regulation of transcription by RNA polymerase I
A	0016787	molecular_function	hydrolase activity
A	0030174	biological_process	regulation of DNA-templated DNA replication initiation
A	0031507	biological_process	heterochromatin formation
A	0032221	cellular_component	Rpd3S complex
A	0033698	cellular_component	Rpd3L complex
A	0034399	cellular_component	nuclear periphery
A	0034503	biological_process	protein localization to nucleolar rDNA repeats
A	0034605	biological_process	cellular response to heat
A	0044804	biological_process	nucleophagy
A	0045128	biological_process	negative regulation of reciprocal meiotic recombination
A	0045944	biological_process	positive regulation of transcription by RNA polymerase II
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	0070211	cellular_component	Snt2C complex
A	0070550	biological_process	rDNA chromatin condensation
A	0070822	cellular_component	Sin3-type complex
B	0003714	molecular_function	transcription corepressor activity
B	0006355	biological_process	regulation of DNA-templated transcription
D	0000122	biological_process	negative regulation of transcription by RNA polymerase II
D	0000123	cellular_component	histone acetyltransferase complex
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0006281	biological_process	DNA repair
D	0006325	biological_process	chromatin organization
D	0006334	biological_process	nucleosome assembly
D	0006335	biological_process	DNA replication-dependent chromatin assembly
D	0006337	biological_process	nucleosome disassembly
D	0006338	biological_process	chromatin remodeling
D	0006351	biological_process	DNA-templated transcription
D	0006355	biological_process	regulation of DNA-templated transcription
D	0006357	biological_process	regulation of transcription by RNA polymerase II
D	0006368	biological_process	transcription elongation by RNA polymerase II
D	0009889	biological_process	regulation of biosynthetic process
D	0030174	biological_process	regulation of DNA-templated DNA replication initiation
D	0032221	cellular_component	Rpd3S complex
D	0032968	biological_process	positive regulation of transcription elongation by RNA polymerase II
D	0035064	molecular_function	methylated histone binding
D	0035267	cellular_component	NuA4 histone acetyltransferase complex
D	0043487	biological_process	regulation of RNA stability
D	0045892	biological_process	negative regulation of DNA-templated transcription
D	0060195	biological_process	negative regulation of antisense RNA transcription
D	1990453	cellular_component	nucleosome disassembly/reassembly complex
E	0000118	cellular_component	histone deacetylase complex
E	0000122	biological_process	negative regulation of transcription by RNA polymerase II
E	0005634	cellular_component	nucleus
E	0006325	biological_process	chromatin organization
E	0006334	biological_process	nucleosome assembly
E	0006357	biological_process	regulation of transcription by RNA polymerase II
E	0006368	biological_process	transcription elongation by RNA polymerase II
E	0008270	molecular_function	zinc ion binding
E	0030174	biological_process	regulation of DNA-templated DNA replication initiation
E	0032221	cellular_component	Rpd3S complex
E	0045944	biological_process	positive regulation of transcription by RNA polymerase II
E	0046872	molecular_function	metal ion binding
E	0060195	biological_process	negative regulation of antisense RNA transcription
F	0000122	biological_process	negative regulation of transcription by RNA polymerase II
F	0000123	cellular_component	histone acetyltransferase complex
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0006281	biological_process	DNA repair
F	0006325	biological_process	chromatin organization
F	0006334	biological_process	nucleosome assembly
F	0006335	biological_process	DNA replication-dependent chromatin assembly
F	0006337	biological_process	nucleosome disassembly
F	0006338	biological_process	chromatin remodeling
F	0006351	biological_process	DNA-templated transcription
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	0009889	biological_process	regulation of biosynthetic process
F	0030174	biological_process	regulation of DNA-templated DNA replication initiation
F	0032221	cellular_component	Rpd3S complex
F	0032968	biological_process	positive regulation of transcription elongation by RNA polymerase II
F	0035064	molecular_function	methylated histone binding
F	0035267	cellular_component	NuA4 histone acetyltransferase complex
F	0043487	biological_process	regulation of RNA stability
F	0045892	biological_process	negative regulation of DNA-templated transcription
F	0060195	biological_process	negative regulation of antisense RNA transcription
F	1990453	cellular_component	nucleosome disassembly/reassembly complex
G	0000118	cellular_component	histone deacetylase complex
G	0000122	biological_process	negative regulation of transcription by RNA polymerase II
G	0005634	cellular_component	nucleus
G	0006325	biological_process	chromatin organization
G	0006334	biological_process	nucleosome assembly
G	0006357	biological_process	regulation of transcription by RNA polymerase II
G	0006368	biological_process	transcription elongation by RNA polymerase II
G	0008270	molecular_function	zinc ion binding
G	0030174	biological_process	regulation of DNA-templated DNA replication initiation
G	0032221	cellular_component	Rpd3S complex
G	0045944	biological_process	positive regulation of transcription by RNA polymerase II
G	0046872	molecular_function	metal ion binding
G	0060195	biological_process	negative regulation of antisense RNA transcription
O	0000786	cellular_component	nucleosome
O	0003677	molecular_function	DNA binding
O	0005515	molecular_function	protein binding
O	0005634	cellular_component	nucleus
O	0005654	cellular_component	nucleoplasm
O	0005694	cellular_component	chromosome
O	0030527	molecular_function	structural constituent of chromatin
O	0046982	molecular_function	protein heterodimerization activity
P	0000786	cellular_component	nucleosome
P	0003677	molecular_function	DNA binding
P	0005515	molecular_function	protein binding
P	0005634	cellular_component	nucleus
P	0005694	cellular_component	chromosome
P	0006334	biological_process	nucleosome assembly
P	0030527	molecular_function	structural constituent of chromatin
P	0046982	molecular_function	protein heterodimerization activity
Q	0000786	cellular_component	nucleosome
Q	0003677	molecular_function	DNA binding
Q	0005634	cellular_component	nucleus
Q	0005694	cellular_component	chromosome
Q	0030527	molecular_function	structural constituent of chromatin
Q	0046982	molecular_function	protein heterodimerization activity
R	0000786	cellular_component	nucleosome
R	0003677	molecular_function	DNA binding
R	0005515	molecular_function	protein binding
R	0005634	cellular_component	nucleus
R	0005694	cellular_component	chromosome
R	0030527	molecular_function	structural constituent of chromatin
R	0046982	molecular_function	protein heterodimerization activity
S	0000786	cellular_component	nucleosome
S	0003677	molecular_function	DNA binding
S	0005515	molecular_function	protein binding
S	0005634	cellular_component	nucleus
S	0005654	cellular_component	nucleoplasm
S	0005694	cellular_component	chromosome
S	0030527	molecular_function	structural constituent of chromatin
S	0046982	molecular_function	protein heterodimerization activity
T	0000786	cellular_component	nucleosome
T	0003677	molecular_function	DNA binding
T	0005515	molecular_function	protein binding
T	0005634	cellular_component	nucleus
T	0005694	cellular_component	chromosome
T	0006334	biological_process	nucleosome assembly
T	0030527	molecular_function	structural constituent of chromatin
T	0046982	molecular_function	protein heterodimerization activity
U	0000786	cellular_component	nucleosome
U	0003677	molecular_function	DNA binding
U	0005634	cellular_component	nucleus
U	0005694	cellular_component	chromosome
U	0030527	molecular_function	structural constituent of chromatin
U	0046982	molecular_function	protein heterodimerization activity
V	0000786	cellular_component	nucleosome
V	0003677	molecular_function	DNA binding
V	0005515	molecular_function	protein binding
V	0005634	cellular_component	nucleus
V	0005694	cellular_component	chromosome
V	0030527	molecular_function	structural constituent of chromatin
V	0046982	molecular_function	protein heterodimerization activity

Functional Information from PROSITE/UniProt

site_id	PS00046
Number of Residues	7
Details	HISTONE_H2A Histone H2A signature. AGLqFPV

Chain	Residue	Details
Q	ALA21-VAL27

site_id	PS00047
Number of Residues	5
Details	HISTONE_H4 Histone H4 signature. GAKRH

Chain	Residue	Details
P	GLY14-HIS18

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

Chain	Residue	Details
O	LYS14-LEU20

site_id	PS00357
Number of Residues	23
Details	HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG

Chain	Residue	Details
R	ARG89-GLY111

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

Chain	Residue	Details
O	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
E	CYS263-CYS306

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000250

Chain	Residue	Details
Q	SER1
U	SER1
S	ARG2
S	ARG17
V	LYS2
V	LYS9
V	LYS12
V	LYS17

site_id	SWS_FT_FI2
Number of Residues	2
Details	MOD_RES: N6-acetyllysine => ECO:0000250

Chain	Residue	Details
Q	LYS5
U	LYS5

site_id	SWS_FT_FI3
Number of Residues	4
Details	MOD_RES: N6-succinyllysine => ECO:0000250\|UniProtKB:P0C0S8

Chain	Residue	Details
Q	LYS9
Q	LYS95
U	LYS9
U	LYS95

site_id	SWS_FT_FI4
Number of Residues	2
Details	MOD_RES: N6-(2-hydroxyisobutyryl)lysine; alternate => ECO:0000250\|UniProtKB:P0C0S8

Chain	Residue	Details
Q	LYS36
U	LYS36
V	LYS117

site_id	SWS_FT_FI5
Number of Residues	4
Details	MOD_RES: N6-(2-hydroxyisobutyryl)lysine => ECO:0000250\|UniProtKB:P0C0S8

Chain	Residue	Details
Q	LYS74
Q	LYS75
U	LYS74
U	LYS75
T	LYS8
T	LYS16
T	LYS44
T	LYS79

site_id	SWS_FT_FI6
Number of Residues	2
Details	MOD_RES: N5-methylglutamine => ECO:0000250

Chain	Residue	Details
Q	GLN104
U	GLN104
T	LYS12
T	LYS20

site_id	SWS_FT_FI7
Number of Residues	2
Details	MOD_RES: N6-glutaryllysine; alternate => ECO:0000250\|UniProtKB:P0C0S8

Chain	Residue	Details
Q	LYS118
U	LYS118
T	LYS31
T	LYS91

site_id	SWS_FT_FI8
Number of Residues	8
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250

Chain	Residue	Details
Q	LYS13
S	SER10
Q	LYS15
Q	LYS119
U	LYS13
U	LYS15
U	LYS119

site_id	SWS_FT_FI9
Number of Residues	2
Details	MOD_RES: N6-lactoyllysine; alternate => ECO:0000250\|UniProtKB:P84228

Chain	Residue	Details
O	LYS14
S	LYS14
T	TYR51
T	TYR88

site_id	SWS_FT_FI10
Number of Residues	10
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
O	LYS18
S	LYS64
O	LYS23
O	LYS27
O	M3L36
O	LYS64
S	LYS18
S	LYS23
S	LYS27
S	M3L36

site_id	SWS_FT_FI11
Number of Residues	2
Details	MOD_RES: Citrulline => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
O	ARG26
S	ARG26

site_id	SWS_FT_FI12
Number of Residues	2
Details	MOD_RES: Phosphoserine; alternate; by AURKB, AURKC and RPS6KA5 => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
O	SER28
S	SER28

site_id	SWS_FT_FI13
Number of Residues	2
Details	MOD_RES: N6-methyllysine => ECO:0000250\|UniProtKB:P68431

Chain	Residue	Details
O	LYS37
S	LYS37
T	LYS91

site_id	SWS_FT_FI14
Number of Residues	2
Details	MOD_RES: Phosphotyrosine => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
O	TYR41
S	TYR41

site_id	SWS_FT_FI15
Number of Residues	4
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000250\|UniProtKB:P84228

Chain	Residue	Details
O	LYS56
O	LYS79
S	LYS56
S	LYS79

site_id	SWS_FT_FI16
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
O	SER57
S	SER57

site_id	SWS_FT_FI17
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
O	THR80
O	THR107
S	THR80
S	THR107

site_id	SWS_FT_FI18
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000250\|UniProtKB:P84243

Chain	Residue	Details
O	SER86
S	SER86

site_id	SWS_FT_FI19
Number of Residues	2
Details	MOD_RES: N6-glutaryllysine; alternate => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
O	LYS115
S	LYS115

site_id	SWS_FT_FI20
Number of Residues	2
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
O	LYS122
S	LYS122

site_id	SWS_FT_FI21
Number of Residues	2
Details	LIPID: S-palmitoyl cysteine => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
O	ALA110
S	ALA110

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