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	0006355	biological_process	regulation of DNA-templated transcription
A	0006357	biological_process	regulation of transcription by RNA polymerase II
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	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	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
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	0009889	biological_process	regulation of biosynthetic process
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	0035064	molecular_function	methylated histone binding
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	1990453	cellular_component	nucleosome disassembly/reassembly complex
D	0000118	cellular_component	histone deacetylase complex
D	0000122	biological_process	negative regulation of transcription by RNA polymerase II
D	0005634	cellular_component	nucleus
D	0006325	biological_process	chromatin organization
D	0006334	biological_process	nucleosome assembly
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	0009889	biological_process	regulation of biosynthetic process
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	0035064	molecular_function	methylated histone binding
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	1990453	cellular_component	nucleosome disassembly/reassembly complex
F	0000118	cellular_component	histone deacetylase complex
F	0000122	biological_process	negative regulation of transcription by RNA polymerase II
F	0005634	cellular_component	nucleus
F	0006325	biological_process	chromatin organization
F	0006334	biological_process	nucleosome assembly
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	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	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	0046982	molecular_function	protein heterodimerization activity
J	0000786	cellular_component	nucleosome
J	0003677	molecular_function	DNA binding
J	0005515	molecular_function	protein binding
J	0005634	cellular_component	nucleus
J	0005694	cellular_component	chromosome
J	0030527	molecular_function	structural constituent of chromatin
J	0046982	molecular_function	protein heterodimerization activity
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	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	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	0046982	molecular_function	protein heterodimerization activity
N	0000786	cellular_component	nucleosome
N	0003677	molecular_function	DNA binding
N	0005515	molecular_function	protein binding
N	0005634	cellular_component	nucleus
N	0005694	cellular_component	chromosome
N	0030527	molecular_function	structural constituent of chromatin
N	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
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	2
Details	MOD_RES: Phosphoserine => ECO:0000250

Chain	Residue	Details
I	SER1
M	SER1
K	ARG2
K	ARG17
N	LYS2
N	LYS9
N	LYS12
N	LYS17

---

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

Chain	Residue	Details
I	LYS5
M	LYS5

---

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

Chain	Residue	Details
I	LYS9
I	LYS95
M	LYS9
M	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
I	LYS36
M	LYS36
N	LYS117

---

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

Chain	Residue	Details
I	LYS74
I	LYS75
M	LYS74
M	LYS75
L	LYS8
L	LYS16
L	LYS44
L	LYS79

---

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

Chain	Residue	Details
I	GLN104
M	GLN104
L	LYS12
L	LYS20

---

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

Chain	Residue	Details
I	LYS118
M	LYS118
L	LYS31
L	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
I	LYS13
K	SER10
I	LYS15
I	LYS119
M	LYS13
M	LYS15
M	LYS119

---

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

Chain	Residue	Details
G	LYS14
K	LYS14
L	TYR51
L	TYR88

---

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

Chain	Residue	Details
G	LYS18
K	LYS64
G	LYS23
G	LYS27
G	M3L36
G	LYS64
K	LYS18
K	LYS23
K	LYS27
K	M3L36

---

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

Chain	Residue	Details
G	ARG26
K	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
G	SER28
K	SER28

---

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

Chain	Residue	Details
G	LYS37
K	LYS37
L	LYS91

---

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

Chain	Residue	Details
G	TYR41
K	TYR41

---

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

Chain	Residue	Details
G	LYS56
G	LYS79
K	LYS56
K	LYS79

---

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

Chain	Residue	Details
G	SER57
K	SER57

---

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

Chain	Residue	Details
G	THR80
G	THR107
K	THR80
K	THR107

---

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

Chain	Residue	Details
G	SER86
K	SER86

---

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

Chain	Residue	Details
G	LYS115
K	LYS115

---

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

Chain	Residue	Details
G	LYS122
K	LYS122

---

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

Chain	Residue	Details
G	CYS110
K	CYS110

---