Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

8KD3

Rpd3S in complex with nucleosome with H3K36MLA modification, H3K9Q mutation and 187bp DNA

This is a non-PDB format compatible entry.

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	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	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
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	0005634	cellular_component	nucleus
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	0005634	cellular_component	nucleus
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	8
Details	MOD_RES: N6-acetyllysine => ECO:0000250\|UniProtKB:P0C1H4

Chain	Residue	Details
R	LYS2
R	LYS9
R	LYS12
R	LYS17
V	LYS2
V	LYS9
V	LYS12
V	LYS17

site_id	SWS_FT_FI2
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000269\|PubMed:12757711

Chain	Residue	Details
R	SER11
V	SER11

site_id	SWS_FT_FI3
Number of Residues	2
Details	CARBOHYD: O-linked (GlcNAc) serine => ECO:0000250\|UniProtKB:P62807

Chain	Residue	Details
R	SER109
V	SER109

site_id	SWS_FT_FI4
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250\|UniProtKB:P0C1H4

Chain	Residue	Details
R	LYS117
T	LYS5
V	LYS117

site_id	SWS_FT_FI5
Number of Residues	8
Details	MOD_RES: N6-propionyllysine; alternate => ECO:0000250\|UniProtKB:P62805

Chain	Residue	Details
P	LYS8
P	LYS16
P	LYS44
P	LYS79
T	LYS8
T	LYS16
T	LYS44
T	LYS79

site_id	SWS_FT_FI6
Number of Residues	4
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000250\|UniProtKB:P62805

Chain	Residue	Details
P	LYS12
P	LYS20
T	LYS12
T	LYS20

site_id	SWS_FT_FI7
Number of Residues	4
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000250\|UniProtKB:P62805

Chain	Residue	Details
P	LYS31
P	LYS91
T	LYS31
T	LYS91

site_id	SWS_FT_FI8
Number of Residues	2
Details	MOD_RES: Phosphoserine; by PAK2 => ECO:0000250\|UniProtKB:P62805

Chain	Residue	Details
P	SER47
T	SER47

site_id	SWS_FT_FI9
Number of Residues	4
Details	MOD_RES: Phosphotyrosine => ECO:0000250\|UniProtKB:P62805

Chain	Residue	Details
P	TYR51
P	TYR88
T	TYR51
T	TYR88

site_id	SWS_FT_FI10
Number of Residues	2
Details	MOD_RES: N6-glutaryllysine; alternate => ECO:0000250\|UniProtKB:P62805

Chain	Residue	Details
P	LYS59
T	LYS59

site_id	SWS_FT_FI11
Number of Residues	2
Details	MOD_RES: N6-succinyllysine => ECO:0000250\|UniProtKB:P62805

Chain	Residue	Details
P	LYS77
T	LYS77

site_id	SWS_FT_FI12
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate => ECO:0000250\|UniProtKB:P62805

Chain	Residue	Details
P	LYS31
T	LYS31

site_id	SWS_FT_FI13
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000250\|UniProtKB:P62805

Chain	Residue	Details
P	LYS91
T	LYS91

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