Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

7YI4

Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in close state

This is a non-PDB format compatible entry.

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	0006351	biological_process	DNA-templated transcription
A	0006355	biological_process	regulation of DNA-templated transcription
A	0006357	biological_process	regulation of transcription by RNA polymerase II
A	0010628	biological_process	positive regulation of gene expression
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	0006351	biological_process	DNA-templated transcription
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	0010557	biological_process	positive regulation of macromolecule biosynthetic process
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
B	0141221	molecular_function	histone deacetylase activity, hydrolytic mechanism
C	0000122	biological_process	negative regulation of transcription by RNA polymerase II
C	0000123	cellular_component	histone acetyltransferase complex
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0006281	biological_process	DNA repair
C	0006325	biological_process	chromatin organization
C	0006334	biological_process	nucleosome assembly
C	0006335	biological_process	DNA replication-dependent chromatin assembly
C	0006337	biological_process	nucleosome disassembly
C	0006338	biological_process	chromatin remodeling
C	0006351	biological_process	DNA-templated transcription
C	0006355	biological_process	regulation of DNA-templated transcription
C	0006357	biological_process	regulation of transcription by RNA polymerase II
C	0006368	biological_process	transcription elongation by RNA polymerase II
C	0006974	biological_process	DNA damage response
C	0030174	biological_process	regulation of DNA-templated DNA replication initiation
C	0032221	cellular_component	Rpd3S complex
C	0032968	biological_process	positive regulation of transcription elongation by RNA polymerase II
C	0035267	cellular_component	NuA4 histone acetyltransferase complex
C	0043487	biological_process	regulation of RNA stability
C	0045892	biological_process	negative regulation of DNA-templated transcription
C	0060195	biological_process	negative regulation of antisense RNA transcription
C	0140003	molecular_function	histone H3K36me3 reader activity
C	0140566	molecular_function	histone reader activity
D	0000118	cellular_component	histone deacetylase complex
D	0000122	biological_process	negative regulation of transcription by RNA polymerase II
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0006325	biological_process	chromatin organization
D	0006334	biological_process	nucleosome assembly
D	0006351	biological_process	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	0008270	molecular_function	zinc ion binding
D	0030174	biological_process	regulation of DNA-templated DNA replication initiation
D	0032221	cellular_component	Rpd3S complex
D	0045944	biological_process	positive regulation of transcription by RNA polymerase II
D	0046872	molecular_function	metal ion binding
D	0060195	biological_process	negative regulation of antisense RNA transcription
E	0000122	biological_process	negative regulation of transcription by RNA polymerase II
E	0000123	cellular_component	histone acetyltransferase complex
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0006281	biological_process	DNA repair
E	0006325	biological_process	chromatin organization
E	0006334	biological_process	nucleosome assembly
E	0006335	biological_process	DNA replication-dependent chromatin assembly
E	0006337	biological_process	nucleosome disassembly
E	0006338	biological_process	chromatin remodeling
E	0006351	biological_process	DNA-templated transcription
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	0006974	biological_process	DNA damage response
E	0030174	biological_process	regulation of DNA-templated DNA replication initiation
E	0032221	cellular_component	Rpd3S complex
E	0032968	biological_process	positive regulation of transcription elongation by RNA polymerase II
E	0035267	cellular_component	NuA4 histone acetyltransferase complex
E	0043487	biological_process	regulation of RNA stability
E	0045892	biological_process	negative regulation of DNA-templated transcription
E	0060195	biological_process	negative regulation of antisense RNA transcription
E	0140003	molecular_function	histone H3K36me3 reader activity
E	0140566	molecular_function	histone reader activity
F	0000118	cellular_component	histone deacetylase complex
F	0000122	biological_process	negative regulation of transcription by RNA polymerase II
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0006325	biological_process	chromatin organization
F	0006334	biological_process	nucleosome assembly
F	0006351	biological_process	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	0008270	molecular_function	zinc ion binding
F	0030174	biological_process	regulation of DNA-templated DNA replication initiation
F	0032221	cellular_component	Rpd3S complex
F	0045944	biological_process	positive regulation of transcription by RNA polymerase II
F	0046872	molecular_function	metal ion binding
F	0060195	biological_process	negative regulation of antisense RNA transcription
G	0000786	cellular_component	nucleosome
G	0003677	molecular_function	DNA binding
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005654	cellular_component	nucleoplasm
G	0005694	cellular_component	chromosome
G	0030527	molecular_function	structural constituent of chromatin
G	0031492	molecular_function	nucleosomal DNA binding
G	0031507	biological_process	heterochromatin formation
G	0046982	molecular_function	protein heterodimerization activity
H	0000786	cellular_component	nucleosome
H	0003677	molecular_function	DNA binding
H	0005515	molecular_function	protein binding
H	0005634	cellular_component	nucleus
H	0005694	cellular_component	chromosome
H	0006334	biological_process	nucleosome assembly
H	0030527	molecular_function	structural constituent of chromatin
H	0031507	biological_process	heterochromatin formation
H	0046982	molecular_function	protein heterodimerization activity
I	0000786	cellular_component	nucleosome
I	0003677	molecular_function	DNA binding
I	0005634	cellular_component	nucleus
I	0005694	cellular_component	chromosome
I	0030527	molecular_function	structural constituent of chromatin
I	0031507	biological_process	heterochromatin formation
I	0046982	molecular_function	protein heterodimerization activity
J	0000786	cellular_component	nucleosome
J	0002227	biological_process	innate immune response in mucosa
J	0003677	molecular_function	DNA binding
J	0005515	molecular_function	protein binding
J	0005615	cellular_component	extracellular space
J	0005634	cellular_component	nucleus
J	0005694	cellular_component	chromosome
J	0006325	biological_process	chromatin organization
J	0019731	biological_process	antibacterial humoral response
J	0030527	molecular_function	structural constituent of chromatin
J	0031507	biological_process	heterochromatin formation
J	0046982	molecular_function	protein heterodimerization activity
J	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
K	0000786	cellular_component	nucleosome
K	0003677	molecular_function	DNA binding
K	0005515	molecular_function	protein binding
K	0005634	cellular_component	nucleus
K	0005654	cellular_component	nucleoplasm
K	0005694	cellular_component	chromosome
K	0030527	molecular_function	structural constituent of chromatin
K	0031492	molecular_function	nucleosomal DNA binding
K	0031507	biological_process	heterochromatin formation
K	0046982	molecular_function	protein heterodimerization activity
L	0000786	cellular_component	nucleosome
L	0003677	molecular_function	DNA binding
L	0005515	molecular_function	protein binding
L	0005634	cellular_component	nucleus
L	0005694	cellular_component	chromosome
L	0006334	biological_process	nucleosome assembly
L	0030527	molecular_function	structural constituent of chromatin
L	0031507	biological_process	heterochromatin formation
L	0046982	molecular_function	protein heterodimerization activity
M	0000786	cellular_component	nucleosome
M	0003677	molecular_function	DNA binding
M	0005634	cellular_component	nucleus
M	0005694	cellular_component	chromosome
M	0030527	molecular_function	structural constituent of chromatin
M	0031507	biological_process	heterochromatin formation
M	0046982	molecular_function	protein heterodimerization activity
N	0000786	cellular_component	nucleosome
N	0002227	biological_process	innate immune response in mucosa
N	0003677	molecular_function	DNA binding
N	0005515	molecular_function	protein binding
N	0005615	cellular_component	extracellular space
N	0005634	cellular_component	nucleus
N	0005694	cellular_component	chromosome
N	0006325	biological_process	chromatin organization
N	0019731	biological_process	antibacterial humoral response
N	0030527	molecular_function	structural constituent of chromatin
N	0031507	biological_process	heterochromatin formation
N	0046982	molecular_function	protein heterodimerization activity
N	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
I	ALA21-VAL27

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

Chain	Residue	Details
H	GLY14-HIS18

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

Chain	Residue	Details
G	LYS14-LEU20

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

Chain	Residue	Details
J	ARG89-GLY111

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

Chain	Residue	Details
G	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
D	CYS263-CYS306

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	312
Details	Region: {"description":"Histone deacetylase"}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	20
Details	Motif: {"description":"ESA1-RPD3 motif"}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	1
Details	Active site: {"evidences":[{"evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	49
Details	Zinc finger: {"description":"PHD-type 1","evidences":[{"source":"PROSITE-ProRule","id":"PRU00146","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	58
Details	Zinc finger: {"description":"PHD-type 2; atypical","evidences":[{"source":"PROSITE-ProRule","id":"PRU00146","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	4
Details	Modified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine; by PAK2","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	4
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	2
Details	Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	2
Details	Modified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine; alternate","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	4
Details	Modified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI17
Number of Residues	2
Details	Modified residue: {"description":"N5-methylglutamine","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI18
Number of Residues	2
Details	Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	6
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI20
Number of Residues	2
Details	Glycosylation: {"description":"O-linked (GlcNAc) serine","evidences":[{"source":"UniProtKB","id":"P62807","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI21
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"UniProtKB","id":"P0C1H4","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI22
Number of Residues	4
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI23
Number of Residues	2
Details	Modified residue: {"description":"N6-methyllysine","evidences":[{"source":"UniProtKB","id":"P68431","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI24
Number of Residues	2
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI25
Number of Residues	4
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84228","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI26
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI27
Number of Residues	4
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI28
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI29
Number of Residues	2
Details	Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI30
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI31
Number of Residues	2
Details	Lipidation: {"description":"S-palmitoyl cysteine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

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