8JHO

Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome

Functional Information from GO Data

Chain	GOid	namespace	contents
a	0000786	cellular_component	nucleosome
a	0003677	molecular_function	DNA binding
a	0005515	molecular_function	protein binding
a	0005634	cellular_component	nucleus
a	0005654	cellular_component	nucleoplasm
a	0005694	cellular_component	chromosome
a	0030527	molecular_function	structural constituent of chromatin
a	0046982	molecular_function	protein heterodimerization activity
A	0000786	cellular_component	nucleosome
A	0003677	molecular_function	DNA binding
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005694	cellular_component	chromosome
A	0030527	molecular_function	structural constituent of chromatin
A	0046982	molecular_function	protein heterodimerization activity
b	0000786	cellular_component	nucleosome
b	0003677	molecular_function	DNA binding
b	0005515	molecular_function	protein binding
b	0005634	cellular_component	nucleus
b	0005694	cellular_component	chromosome
b	0006334	biological_process	nucleosome assembly
b	0030527	molecular_function	structural constituent of chromatin
b	0046982	molecular_function	protein heterodimerization activity
B	0000786	cellular_component	nucleosome
B	0003677	molecular_function	DNA binding
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005694	cellular_component	chromosome
B	0006334	biological_process	nucleosome assembly
B	0030527	molecular_function	structural constituent of chromatin
B	0046982	molecular_function	protein heterodimerization activity
c	0000786	cellular_component	nucleosome
c	0003677	molecular_function	DNA binding
c	0005634	cellular_component	nucleus
c	0005694	cellular_component	chromosome
c	0030527	molecular_function	structural constituent of chromatin
c	0046982	molecular_function	protein heterodimerization activity
C	0000786	cellular_component	nucleosome
C	0003677	molecular_function	DNA binding
C	0005634	cellular_component	nucleus
C	0005694	cellular_component	chromosome
C	0030527	molecular_function	structural constituent of chromatin
C	0046982	molecular_function	protein heterodimerization activity
d	0000786	cellular_component	nucleosome
d	0003677	molecular_function	DNA binding
d	0005515	molecular_function	protein binding
d	0005634	cellular_component	nucleus
d	0005694	cellular_component	chromosome
d	0030527	molecular_function	structural constituent of chromatin
d	0046982	molecular_function	protein heterodimerization activity
D	0000786	cellular_component	nucleosome
D	0003677	molecular_function	DNA binding
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005694	cellular_component	chromosome
D	0030527	molecular_function	structural constituent of chromatin
D	0046982	molecular_function	protein heterodimerization activity
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
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
f	0000786	cellular_component	nucleosome
f	0003677	molecular_function	DNA binding
f	0005515	molecular_function	protein binding
f	0005634	cellular_component	nucleus
f	0005694	cellular_component	chromosome
f	0006334	biological_process	nucleosome assembly
f	0030527	molecular_function	structural constituent of chromatin
f	0046982	molecular_function	protein heterodimerization activity
F	0000786	cellular_component	nucleosome
F	0003677	molecular_function	DNA binding
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005694	cellular_component	chromosome
F	0006334	biological_process	nucleosome assembly
F	0030527	molecular_function	structural constituent of chromatin
F	0046982	molecular_function	protein heterodimerization activity
g	0000786	cellular_component	nucleosome
g	0003677	molecular_function	DNA binding
g	0005634	cellular_component	nucleus
g	0005694	cellular_component	chromosome
g	0030527	molecular_function	structural constituent of chromatin
g	0046982	molecular_function	protein heterodimerization activity
G	0000786	cellular_component	nucleosome
G	0003677	molecular_function	DNA binding
G	0005634	cellular_component	nucleus
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	0030527	molecular_function	structural constituent of chromatin
h	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	0030527	molecular_function	structural constituent of chromatin
H	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	PS00046
Number of Residues	7
Details	HISTONE_H2A Histone H2A signature. AGLqFPV

Chain	Residue	Details
C	ALA21-VAL27

---

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

Chain	Residue	Details
B	GLY14-HIS18

---

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

Chain	Residue	Details
A	LYS14-LEU20

---

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

Chain	Residue	Details
D	ARG89-GLY111

---

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

Chain	Residue	Details
A	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
d	LYS9
d	LYS12
d	LYS17
h	LYS2
h	LYS9
h	LYS12
h	LYS17
P	GLU260-LYS309
D	LYS12
D	LYS17
H	LYS2
H	LYS9
H	LYS12
H	LYS17
d	LYS2

---

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
d	SER11
h	SER11

---

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
d	SER109
h	SER109
c	LYS9
c	LYS95
g	LYS9
g	LYS95

---

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

Chain	Residue	Details
N	SER68
P	SER68
H	LYS117
g	LYS36
d	LYS117
h	LYS117

---

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
b	LYS16
b	LYS44
b	LYS79
f	LYS8
f	LYS16
f	LYS44
f	LYS79
P	SER683
G	LYS74
G	LYS75
c	LYS74
c	LYS75
g	LYS74
g	LYS75
b	LYS8

---

site_id	SWS_FT_FI6
Number of Residues	4
Details	MOD_RES: N5-methylglutamine => ECO:0000250

Chain	Residue	Details
C	GLN104
G	GLN104
c	GLN104
g	GLN104
b	LYS12
b	LYS20
f	LYS12
f	LYS20

---

site_id	SWS_FT_FI7
Number of Residues	4
Details	MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P0C0S8

Chain	Residue	Details
C	LYS118
G	LYS118
c	LYS118
g	LYS118
b	LYS31
b	LYS91
f	LYS31
f	LYS91

---

site_id	SWS_FT_FI8
Number of Residues	16
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250

Chain	Residue	Details
C	LYS13
c	LYS15
c	LYS119
g	LYS13
g	LYS15
g	LYS119
F	SER47
C	LYS15
C	LYS119
G	LYS13
G	LYS15
G	LYS119
c	LYS13

---

site_id	SWS_FT_FI9
Number of Residues	8
Details	MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P62805

Chain	Residue	Details
B	TYR51
B	TYR88
F	TYR51
F	TYR88
b	TYR51
b	TYR88
f	TYR51
f	TYR88

---

site_id	SWS_FT_FI10
Number of Residues	4
Details	MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P62805

Chain	Residue	Details
B	LYS59
E	LYS64
a	LYS18
a	LYS23
a	LYS27
a	ML336
a	LYS64
e	LYS18
e	LYS23
e	LYS27
e	ML336
F	LYS59
e	LYS64
b	LYS59
f	LYS59
A	LYS64
E	LYS18
E	LYS23
E	LYS27
E	ML336

---

site_id	SWS_FT_FI11
Number of Residues	4
Details	MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P62805

Chain	Residue	Details
B	LYS77
F	LYS77
b	LYS77
f	LYS77

---

site_id	SWS_FT_FI12
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate => ECO:0000250|UniProtKB:P62805

Chain	Residue	Details
B	LYS31
F	LYS31
b	LYS31
f	LYS31

---

site_id	SWS_FT_FI13
Number of Residues	8
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000250|UniProtKB:P62805

Chain	Residue	Details
A	LYS37
B	LYS91
a	LYS37
F	LYS91
b	LYS91
f	LYS91

---

site_id	SWS_FT_FI14
Number of Residues	4
Details	MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:Q71DI3

Chain	Residue	Details
A	TYR41
E	TYR41
a	TYR41
e	TYR41

---

site_id	SWS_FT_FI15
Number of Residues	8
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84228

Chain	Residue	Details
A	LYS56
A	LYS79
E	LYS56
E	LYS79
a	LYS56
a	LYS79
e	LYS56
e	LYS79

---

site_id	SWS_FT_FI16
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q71DI3

Chain	Residue	Details
A	SER57
E	SER57
a	SER57
e	SER57

---

site_id	SWS_FT_FI17
Number of Residues	8
Details	MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3

Chain	Residue	Details
A	THR80
A	THR107
E	THR80
E	THR107
a	THR80
a	THR107
e	THR80
e	THR107

---

site_id	SWS_FT_FI18
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243

Chain	Residue	Details
A	SER86
E	SER86
a	SER86
e	SER86

---

site_id	SWS_FT_FI19
Number of Residues	4
Details	MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:Q71DI3

Chain	Residue	Details
A	LYS115
E	LYS115
a	LYS115
e	LYS115

---

site_id	SWS_FT_FI20
Number of Residues	4
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q71DI3

Chain	Residue	Details
A	LYS122
E	LYS122
a	LYS122
e	LYS122

---

site_id	SWS_FT_FI21
Number of Residues	4
Details	LIPID: S-palmitoyl cysteine => ECO:0000250|UniProtKB:Q71DI3

Chain	Residue	Details
A	ALA110
E	ALA110
a	ALA110
e	ALA110

---