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8W9F

Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3

Functional Information from GO Data
ChainGOidnamespacecontents
a0000786cellular_componentnucleosome
a0003677molecular_functionDNA binding
a0005515molecular_functionprotein binding
a0005576cellular_componentextracellular region
a0005634cellular_componentnucleus
a0005654cellular_componentnucleoplasm
a0005694cellular_componentchromosome
a0006325biological_processchromatin organization
a0006334biological_processnucleosome assembly
a0010467biological_processgene expression
a0016020cellular_componentmembrane
a0032200biological_processtelomere organization
a0032991cellular_componentprotein-containing complex
a0040029biological_processepigenetic regulation of gene expression
a0043229cellular_componentintracellular organelle
a0045296molecular_functioncadherin binding
a0070062cellular_componentextracellular exosome
A0000086biological_processG2/M transition of mitotic cell cycle
A0000122biological_processnegative regulation of transcription by RNA polymerase II
A0000785cellular_componentchromatin
A0003713molecular_functiontranscription coactivator activity
A0003714molecular_functiontranscription corepressor activity
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0006303biological_processdouble-strand break repair via nonhomologous end joining
A0006325biological_processchromatin organization
A0006334biological_processnucleosome assembly
A0006357biological_processregulation of transcription by RNA polymerase II
A0016479biological_processnegative regulation of transcription by RNA polymerase I
A0030174biological_processregulation of DNA-templated DNA replication initiation
A0032221cellular_componentRpd3S complex
A0033698cellular_componentRpd3L complex
A0034605biological_processcellular response to heat
A0042802molecular_functionidentical protein binding
A0044804biological_processnucleophagy
A0045944biological_processpositive regulation of transcription by RNA polymerase II
A0051301biological_processcell division
A0051321biological_processmeiotic cell cycle
A0061186biological_processnegative regulation of silent mating-type cassette heterochromatin formation
A0061188biological_processnegative regulation of rDNA heterochromatin formation
A0070210cellular_componentRpd3L-Expanded complex
A0070550biological_processrDNA chromatin condensation
A0070822cellular_componentSin3-type complex
b0000781cellular_componentchromosome, telomeric region
b0000786cellular_componentnucleosome
b0003677molecular_functionDNA binding
b0003723molecular_functionRNA binding
b0005515molecular_functionprotein binding
b0005576cellular_componentextracellular region
b0005634cellular_componentnucleus
b0005654cellular_componentnucleoplasm
b0005694cellular_componentchromosome
b0006325biological_processchromatin organization
b0006334biological_processnucleosome assembly
b0016020cellular_componentmembrane
b0030527molecular_functionstructural constituent of chromatin
b0032200biological_processtelomere organization
b0032991cellular_componentprotein-containing complex
b0043505cellular_componentCENP-A containing nucleosome
b0045653biological_processnegative regulation of megakaryocyte differentiation
b0061644biological_processprotein localization to CENP-A containing chromatin
b0070062cellular_componentextracellular exosome
B0000082biological_processG1/S transition of mitotic cell cycle
B0000086biological_processG2/M transition of mitotic cell cycle
B0000118cellular_componenthistone deacetylase complex
B0000122biological_processnegative regulation of transcription by RNA polymerase II
B0003713molecular_functiontranscription coactivator activity
B0003714molecular_functiontranscription corepressor activity
B0004407molecular_functionhistone deacetylase activity
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005737cellular_componentcytoplasm
B0006325biological_processchromatin organization
B0006334biological_processnucleosome assembly
B0006355biological_processregulation of DNA-templated transcription
B0006357biological_processregulation of transcription by RNA polymerase II
B0006368biological_processtranscription elongation by RNA polymerase II
B0006979biological_processresponse to oxidative stress
B0006995biological_processcellular response to nitrogen starvation
B0008270molecular_functionzinc ion binding
B0016239biological_processpositive regulation of macroautophagy
B0016479biological_processnegative regulation of transcription by RNA polymerase I
B0016787molecular_functionhydrolase activity
B0030174biological_processregulation of DNA-templated DNA replication initiation
B0031507biological_processheterochromatin formation
B0032221cellular_componentRpd3S complex
B0033698cellular_componentRpd3L complex
B0034399cellular_componentnuclear periphery
B0034503biological_processprotein localization to nucleolar rDNA repeats
B0034605biological_processcellular response to heat
B0044804biological_processnucleophagy
B0045128biological_processnegative regulation of reciprocal meiotic recombination
B0045944biological_processpositive regulation of transcription by RNA polymerase II
B0051321biological_processmeiotic cell cycle
B0061186biological_processnegative regulation of silent mating-type cassette heterochromatin formation
B0061188biological_processnegative regulation of rDNA heterochromatin formation
B0070210cellular_componentRpd3L-Expanded complex
B0070211cellular_componentSnt2C complex
B0070550biological_processrDNA chromatin condensation
B0070822cellular_componentSin3-type complex
c0000786cellular_componentnucleosome
c0003677molecular_functionDNA binding
c0005515molecular_functionprotein binding
c0005634cellular_componentnucleus
c0005694cellular_componentchromosome
c0006325biological_processchromatin organization
c0008285biological_processnegative regulation of cell population proliferation
c0031492molecular_functionnucleosomal DNA binding
c0031507biological_processheterochromatin formation
c0043229cellular_componentintracellular organelle
c0043505cellular_componentCENP-A containing nucleosome
c0061644biological_processprotein localization to CENP-A containing chromatin
c0070062cellular_componentextracellular exosome
C0000122biological_processnegative regulation of transcription by RNA polymerase II
C0000123cellular_componenthistone acetyltransferase complex
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0006281biological_processDNA repair
C0006325biological_processchromatin organization
C0006334biological_processnucleosome assembly
C0006335biological_processDNA replication-dependent chromatin assembly
C0006337biological_processnucleosome disassembly
C0006338biological_processchromatin remodeling
C0006351biological_processDNA-templated transcription
C0006357biological_processregulation of transcription by RNA polymerase II
C0006368biological_processtranscription elongation by RNA polymerase II
C0009889biological_processregulation of biosynthetic process
C0030174biological_processregulation of DNA-templated DNA replication initiation
C0032221cellular_componentRpd3S complex
C0032968biological_processpositive regulation of transcription elongation by RNA polymerase II
C0035064molecular_functionmethylated histone binding
C0035267cellular_componentNuA4 histone acetyltransferase complex
C0043487biological_processregulation of RNA stability
C0045892biological_processnegative regulation of DNA-templated transcription
C0060195biological_processnegative regulation of antisense RNA transcription
C1990453cellular_componentnucleosome disassembly/reassembly complex
d0000786cellular_componentnucleosome
d0002227biological_processinnate immune response in mucosa
d0003674molecular_functionmolecular_function
d0003677molecular_functionDNA binding
d0005515molecular_functionprotein binding
d0005615cellular_componentextracellular space
d0005634cellular_componentnucleus
d0005654cellular_componentnucleoplasm
d0005694cellular_componentchromosome
d0005829cellular_componentcytosol
d0019731biological_processantibacterial humoral response
d0031640biological_processkilling of cells of another organism
d0042742biological_processdefense response to bacterium
d0043229cellular_componentintracellular organelle
d0050829biological_processdefense response to Gram-negative bacterium
d0050830biological_processdefense response to Gram-positive bacterium
d0061844biological_processantimicrobial humoral immune response mediated by antimicrobial peptide
D0000122biological_processnegative regulation of transcription by RNA polymerase II
D0000123cellular_componenthistone acetyltransferase complex
D0005515molecular_functionprotein binding
D0005634cellular_componentnucleus
D0006281biological_processDNA repair
D0006325biological_processchromatin organization
D0006334biological_processnucleosome assembly
D0006335biological_processDNA replication-dependent chromatin assembly
D0006337biological_processnucleosome disassembly
D0006338biological_processchromatin remodeling
D0006351biological_processDNA-templated transcription
D0006357biological_processregulation of transcription by RNA polymerase II
D0006368biological_processtranscription elongation by RNA polymerase II
D0009889biological_processregulation of biosynthetic process
D0030174biological_processregulation of DNA-templated DNA replication initiation
D0032221cellular_componentRpd3S complex
D0032968biological_processpositive regulation of transcription elongation by RNA polymerase II
D0035064molecular_functionmethylated histone binding
D0035267cellular_componentNuA4 histone acetyltransferase complex
D0043487biological_processregulation of RNA stability
D0045892biological_processnegative regulation of DNA-templated transcription
D0060195biological_processnegative regulation of antisense RNA transcription
D1990453cellular_componentnucleosome disassembly/reassembly complex
e0000786cellular_componentnucleosome
e0003677molecular_functionDNA binding
e0005515molecular_functionprotein binding
e0005576cellular_componentextracellular region
e0005634cellular_componentnucleus
e0005654cellular_componentnucleoplasm
e0005694cellular_componentchromosome
e0006325biological_processchromatin organization
e0006334biological_processnucleosome assembly
e0010467biological_processgene expression
e0016020cellular_componentmembrane
e0032200biological_processtelomere organization
e0032991cellular_componentprotein-containing complex
e0040029biological_processepigenetic regulation of gene expression
e0043229cellular_componentintracellular organelle
e0045296molecular_functioncadherin binding
e0070062cellular_componentextracellular exosome
E0000118cellular_componenthistone deacetylase complex
E0000122biological_processnegative regulation of transcription by RNA polymerase II
E0005634cellular_componentnucleus
E0006325biological_processchromatin organization
E0006334biological_processnucleosome assembly
E0006357biological_processregulation of transcription by RNA polymerase II
E0006368biological_processtranscription elongation by RNA polymerase II
E0008270molecular_functionzinc ion binding
E0030174biological_processregulation of DNA-templated DNA replication initiation
E0032221cellular_componentRpd3S complex
E0045944biological_processpositive regulation of transcription by RNA polymerase II
E0046872molecular_functionmetal ion binding
E0060195biological_processnegative regulation of antisense RNA transcription
f0000781cellular_componentchromosome, telomeric region
f0000786cellular_componentnucleosome
f0003677molecular_functionDNA binding
f0003723molecular_functionRNA binding
f0005515molecular_functionprotein binding
f0005576cellular_componentextracellular region
f0005634cellular_componentnucleus
f0005654cellular_componentnucleoplasm
f0005694cellular_componentchromosome
f0006325biological_processchromatin organization
f0006334biological_processnucleosome assembly
f0016020cellular_componentmembrane
f0030527molecular_functionstructural constituent of chromatin
f0032200biological_processtelomere organization
f0032991cellular_componentprotein-containing complex
f0043505cellular_componentCENP-A containing nucleosome
f0045653biological_processnegative regulation of megakaryocyte differentiation
f0061644biological_processprotein localization to CENP-A containing chromatin
f0070062cellular_componentextracellular exosome
F0000118cellular_componenthistone deacetylase complex
F0000122biological_processnegative regulation of transcription by RNA polymerase II
F0005634cellular_componentnucleus
F0006325biological_processchromatin organization
F0006334biological_processnucleosome assembly
F0006357biological_processregulation of transcription by RNA polymerase II
F0006368biological_processtranscription elongation by RNA polymerase II
F0008270molecular_functionzinc ion binding
F0030174biological_processregulation of DNA-templated DNA replication initiation
F0032221cellular_componentRpd3S complex
F0045944biological_processpositive regulation of transcription by RNA polymerase II
F0046872molecular_functionmetal ion binding
F0060195biological_processnegative regulation of antisense RNA transcription
g0000786cellular_componentnucleosome
g0003677molecular_functionDNA binding
g0005515molecular_functionprotein binding
g0005634cellular_componentnucleus
g0005694cellular_componentchromosome
g0006325biological_processchromatin organization
g0008285biological_processnegative regulation of cell population proliferation
g0031492molecular_functionnucleosomal DNA binding
g0031507biological_processheterochromatin formation
g0043229cellular_componentintracellular organelle
g0043505cellular_componentCENP-A containing nucleosome
g0061644biological_processprotein localization to CENP-A containing chromatin
g0070062cellular_componentextracellular exosome
G0000122biological_processnegative regulation of transcription by RNA polymerase II
G0000123cellular_componenthistone acetyltransferase complex
G0005515molecular_functionprotein binding
G0005634cellular_componentnucleus
G0006281biological_processDNA repair
G0006325biological_processchromatin organization
G0006334biological_processnucleosome assembly
G0006335biological_processDNA replication-dependent chromatin assembly
G0006337biological_processnucleosome disassembly
G0006338biological_processchromatin remodeling
G0006351biological_processDNA-templated transcription
G0006357biological_processregulation of transcription by RNA polymerase II
G0006368biological_processtranscription elongation by RNA polymerase II
G0009889biological_processregulation of biosynthetic process
G0030174biological_processregulation of DNA-templated DNA replication initiation
G0032221cellular_componentRpd3S complex
G0032968biological_processpositive regulation of transcription elongation by RNA polymerase II
G0035064molecular_functionmethylated histone binding
G0035267cellular_componentNuA4 histone acetyltransferase complex
G0043487biological_processregulation of RNA stability
G0045892biological_processnegative regulation of DNA-templated transcription
G0060195biological_processnegative regulation of antisense RNA transcription
G1990453cellular_componentnucleosome disassembly/reassembly complex
h0000786cellular_componentnucleosome
h0002227biological_processinnate immune response in mucosa
h0003674molecular_functionmolecular_function
h0003677molecular_functionDNA binding
h0005515molecular_functionprotein binding
h0005615cellular_componentextracellular space
h0005634cellular_componentnucleus
h0005654cellular_componentnucleoplasm
h0005694cellular_componentchromosome
h0005829cellular_componentcytosol
h0019731biological_processantibacterial humoral response
h0031640biological_processkilling of cells of another organism
h0042742biological_processdefense response to bacterium
h0043229cellular_componentintracellular organelle
h0050829biological_processdefense response to Gram-negative bacterium
h0050830biological_processdefense response to Gram-positive bacterium
h0061844biological_processantimicrobial humoral immune response mediated by antimicrobial peptide
Functional Information from PROSITE/UniProt
site_idPS00046
Number of Residues7
DetailsHISTONE_H2A Histone H2A signature. AGLqFPV
ChainResidueDetails
cALA21-VAL27

site_idPS00047
Number of Residues5
DetailsHISTONE_H4 Histone H4 signature. GAKRH
ChainResidueDetails
bGLY14-HIS18

site_idPS00322
Number of Residues7
DetailsHISTONE_H3_1 Histone H3 signature 1. KAPRKQL
ChainResidueDetails
aLYS14-LEU20

site_idPS00357
Number of Residues23
DetailsHISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG
ChainResidueDetails
dARG92-GLY114

site_idPS00959
Number of Residues9
DetailsHISTONE_H3_2 Histone H3 signature 2. PFqRLVREI
ChainResidueDetails
aPRO66-ILE74

site_idPS01359
Number of Residues44
DetailsZF_PHD_1 Zinc finger PHD-type signature. CsaCnqsgsf.......................................LcCdt..Cpks.FHflCldppidpnnlpkgd...............................WhCneC
ChainResidueDetails
ECYS263-CYS306

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues3
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:19779198
ChainResidueDetails
CSER201
DSER201
GSER201

site_idSWS_FT_FI2
Number of Residues1
DetailsMOD_RES: Phosphothreonine => ECO:0007744|PubMed:17330950, ECO:0007744|PubMed:18407956
ChainResidueDetails
BTHR394
FPHE414-THR472

site_idSWS_FT_FI3
Number of Residues1
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198
ChainResidueDetails
BSER408
hLYS11
hLYS15
hLYS16
hLYS20
hLYS23
hLYS43
hLYS85
FMET1
dLYS15
dLYS16
dLYS20
dLYS23
dLYS43
dLYS85
hLYS5

site_idSWS_FT_FI4
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:18407956
ChainResidueDetails
ESER68
FSER68
gLYS9
gLYS95

site_idSWS_FT_FI5
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198
ChainResidueDetails
ESER683
FSER683
bLYS44
fLYS8
fLYS16
fLYS44

site_idSWS_FT_FI6
Number of Residues2
DetailsMOD_RES: Symmetric dimethylarginine; by PRMT5; alternate => ECO:0000250|UniProtKB:P68433
ChainResidueDetails
aARG8
eARG8
bLYS77
bLYS91
fLYS12
fLYS31
fLYS77
fLYS91

site_idSWS_FT_FI7
Number of Residues2
DetailsMOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:11242053, ECO:0000269|PubMed:16185088, ECO:0000269|PubMed:16267050, ECO:0000269|PubMed:16457588, ECO:0000269|PubMed:17194708
ChainResidueDetails
aLYS9
eLYS9
gLYS74
gLYS75

site_idSWS_FT_FI8
Number of Residues2
DetailsMOD_RES: Phosphoserine; alternate; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5 => ECO:0000269|PubMed:10464286, ECO:0000269|PubMed:11856369, ECO:0000269|PubMed:12560483, ECO:0000269|PubMed:15681610, ECO:0000269|PubMed:16185088, ECO:0000269|PubMed:16457588
ChainResidueDetails
aSER10
eSER10
dLYS120
hLYS34
hLYS116
hLYS120

site_idSWS_FT_FI9
Number of Residues2
DetailsMOD_RES: Phosphothreonine; by PKC and CHEK1 => ECO:0000269|PubMed:12560483, ECO:0000269|PubMed:18066052, ECO:0000269|PubMed:18243098, ECO:0000269|PubMed:22901803
ChainResidueDetails
aTHR11
eTHR11
cLYS125
gLYS118
gLYS119
gLYS125

site_idSWS_FT_FI10
Number of Residues4
DetailsMOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435
ChainResidueDetails
aLYS14
aLYS56
eLYS14
eLYS56

site_idSWS_FT_FI11
Number of Residues2
DetailsMOD_RES: Citrulline; alternate => ECO:0000269|PubMed:15345777, ECO:0000269|PubMed:16497732, ECO:0000269|PubMed:16567635
ChainResidueDetails
aARG17
eARG17
hLYS46
hLYS108

site_idSWS_FT_FI12
Number of Residues4
DetailsMOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:16267050, ECO:0000269|PubMed:17194708
ChainResidueDetails
aLYS18
aLYS64
eLYS18
eLYS64

site_idSWS_FT_FI13
Number of Residues2
DetailsMOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:17194708
ChainResidueDetails
aLYS23
eLYS23

site_idSWS_FT_FI14
Number of Residues2
DetailsMOD_RES: Citrulline => ECO:0000269|PubMed:16567635
ChainResidueDetails
aARG26
eARG26
hARG86
hARG92

site_idSWS_FT_FI15
Number of Residues2
DetailsMOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:16185088, ECO:0000269|PubMed:16267050, ECO:0000269|PubMed:16627869, ECO:0000269|PubMed:17194708
ChainResidueDetails
aLYS27
eLYS27
fLYS91

site_idSWS_FT_FI16
Number of Residues2
DetailsMOD_RES: Phosphoserine; alternate; by AURKB, AURKC and RPS6KA5 => ECO:0000269|PubMed:10464286, ECO:0000269|PubMed:11856369, ECO:0000269|PubMed:15681610, ECO:0000269|PubMed:15684425, ECO:0000269|PubMed:16185088, ECO:0000269|PubMed:16457588
ChainResidueDetails
aSER28
eSER28
bLYS79
fLYS20
fLYS59
fLYS79

site_idSWS_FT_FI17
Number of Residues2
DetailsMOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:15983376, ECO:0000269|PubMed:16185088, ECO:0000269|PubMed:16267050, ECO:0000269|PubMed:16627869, ECO:0000269|PubMed:17194708
ChainResidueDetails
aLYS36
eLYS36

site_idSWS_FT_FI18
Number of Residues2
DetailsMOD_RES: N6-methyllysine => ECO:0000269|PubMed:15983376
ChainResidueDetails
aLYS37
eLYS37
hLYS120

site_idSWS_FT_FI19
Number of Residues2
DetailsMOD_RES: Phosphotyrosine => ECO:0000269|PubMed:19783980
ChainResidueDetails
aTYR41
eTYR41

site_idSWS_FT_FI20
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0000269|PubMed:20850016
ChainResidueDetails
aSER57
eSER57

site_idSWS_FT_FI21
Number of Residues2
DetailsMOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435, ECO:0000269|PubMed:29211711
ChainResidueDetails
aLYS79
eLYS79

site_idSWS_FT_FI22
Number of Residues2
DetailsMOD_RES: Phosphothreonine => ECO:0000269|PubMed:20850016
ChainResidueDetails
aTHR80
eTHR80

site_idSWS_FT_FI23
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243
ChainResidueDetails
aSER86
eSER86

site_idSWS_FT_FI24
Number of Residues2
DetailsMOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3
ChainResidueDetails
aTHR107
eTHR107

site_idSWS_FT_FI25
Number of Residues2
DetailsMOD_RES: N6-glutaryllysine; alternate => ECO:0000269|PubMed:31542297
ChainResidueDetails
aLYS115
eLYS115

site_idSWS_FT_FI26
Number of Residues2
DetailsMOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435, ECO:0000269|PubMed:27436229
ChainResidueDetails
aLYS122
eLYS122

site_idSWS_FT_FI27
Number of Residues2
DetailsLIPID: N6-decanoyllysine => ECO:0000269|PubMed:35939806
ChainResidueDetails
aLYS18
eLYS18

223166

PDB entries from 2024-07-31

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