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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

8TOF

Rpd3S bound to an H3K36Cme3 modified nucleosome

Functional Information from GO Data
ChainGOidnamespacecontents
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
A0006355biological_processregulation of DNA-templated transcription
A0006357biological_processregulation of transcription by RNA polymerase II
A0010558biological_processnegative regulation of macromolecule biosynthetic process
A0010628biological_processpositive regulation of gene expression
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
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
B0010557biological_processpositive regulation of macromolecule biosynthetic process
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
B0141221molecular_functionhistone deacetylase activity, hydrolytic mechanism
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
D0006355biological_processregulation of DNA-templated transcription
D0006357biological_processregulation of transcription by RNA polymerase II
D0006368biological_processtranscription elongation by RNA polymerase II
D0006974biological_processDNA damage response
D0030174biological_processregulation of DNA-templated DNA replication initiation
D0032221cellular_componentRpd3S complex
D0032968biological_processpositive regulation of transcription elongation by RNA polymerase II
D0035267cellular_componentNuA4 histone acetyltransferase complex
D0043487biological_processregulation of RNA stability
D0045892biological_processnegative regulation of DNA-templated transcription
D0060195biological_processnegative regulation of antisense RNA transcription
D0140003molecular_functionhistone H3K36me3 reader activity
D0140566molecular_functionhistone reader activity
D1990453cellular_componentnucleosome disassembly/reassembly complex
E0000122biological_processnegative regulation of transcription by RNA polymerase II
E0000123cellular_componenthistone acetyltransferase complex
E0005515molecular_functionprotein binding
E0005634cellular_componentnucleus
E0006281biological_processDNA repair
E0006325biological_processchromatin organization
E0006334biological_processnucleosome assembly
E0006335biological_processDNA replication-dependent chromatin assembly
E0006337biological_processnucleosome disassembly
E0006338biological_processchromatin remodeling
E0006351biological_processDNA-templated transcription
E0006355biological_processregulation of DNA-templated transcription
E0006357biological_processregulation of transcription by RNA polymerase II
E0006368biological_processtranscription elongation by RNA polymerase II
E0006974biological_processDNA damage response
E0030174biological_processregulation of DNA-templated DNA replication initiation
E0032221cellular_componentRpd3S complex
E0032968biological_processpositive regulation of transcription elongation by RNA polymerase II
E0035267cellular_componentNuA4 histone acetyltransferase complex
E0043487biological_processregulation of RNA stability
E0045892biological_processnegative regulation of DNA-templated transcription
E0060195biological_processnegative regulation of antisense RNA transcription
E0140003molecular_functionhistone H3K36me3 reader activity
E0140566molecular_functionhistone reader activity
E1990453cellular_componentnucleosome disassembly/reassembly complex
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
G0000118cellular_componenthistone deacetylase complex
G0000122biological_processnegative regulation of transcription by RNA polymerase II
G0005634cellular_componentnucleus
G0006325biological_processchromatin organization
G0006334biological_processnucleosome assembly
G0006357biological_processregulation of transcription by RNA polymerase II
G0006368biological_processtranscription elongation by RNA polymerase II
G0008270molecular_functionzinc ion binding
G0030174biological_processregulation of DNA-templated DNA replication initiation
G0032221cellular_componentRpd3S complex
G0045944biological_processpositive regulation of transcription by RNA polymerase II
G0046872molecular_functionmetal ion binding
G0060195biological_processnegative regulation of antisense RNA transcription
a0000786cellular_componentnucleosome
a0003677molecular_functionDNA binding
a0005634cellular_componentnucleus
a0005694cellular_componentchromosome
a0030527molecular_functionstructural constituent of chromatin
a0046982molecular_functionprotein heterodimerization activity
b0000786cellular_componentnucleosome
b0003677molecular_functionDNA binding
b0005515molecular_functionprotein binding
b0005634cellular_componentnucleus
b0005694cellular_componentchromosome
b0006334biological_processnucleosome assembly
b0030527molecular_functionstructural constituent of chromatin
b0046982molecular_functionprotein heterodimerization activity
c0000786cellular_componentnucleosome
c0003677molecular_functionDNA binding
c0005634cellular_componentnucleus
c0005694cellular_componentchromosome
c0030527molecular_functionstructural constituent of chromatin
c0031507biological_processheterochromatin formation
c0046982molecular_functionprotein heterodimerization activity
d0000786cellular_componentnucleosome
d0003677molecular_functionDNA binding
d0005515molecular_functionprotein binding
d0005634cellular_componentnucleus
d0005694cellular_componentchromosome
d0030527molecular_functionstructural constituent of chromatin
d0046982molecular_functionprotein heterodimerization activity
e0000786cellular_componentnucleosome
e0003677molecular_functionDNA binding
e0005634cellular_componentnucleus
e0005694cellular_componentchromosome
e0030527molecular_functionstructural constituent of chromatin
e0046982molecular_functionprotein heterodimerization activity
f0000786cellular_componentnucleosome
f0003677molecular_functionDNA binding
f0005515molecular_functionprotein binding
f0005634cellular_componentnucleus
f0005694cellular_componentchromosome
f0006334biological_processnucleosome assembly
f0030527molecular_functionstructural constituent of chromatin
f0046982molecular_functionprotein heterodimerization activity
g0000786cellular_componentnucleosome
g0003677molecular_functionDNA binding
g0005634cellular_componentnucleus
g0005694cellular_componentchromosome
g0030527molecular_functionstructural constituent of chromatin
g0031507biological_processheterochromatin formation
g0046982molecular_functionprotein heterodimerization activity
h0000786cellular_componentnucleosome
h0003677molecular_functionDNA binding
h0005515molecular_functionprotein binding
h0005634cellular_componentnucleus
h0005694cellular_componentchromosome
h0030527molecular_functionstructural constituent of chromatin
h0046982molecular_functionprotein heterodimerization activity
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
dARG89-GLY111
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
FCYS263-CYS306
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues312
DetailsRegion: {"description":"Histone deacetylase"}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues20
DetailsMotif: {"description":"ESA1-RPD3 motif"}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues1
DetailsActive site: {"evidences":[{"evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues18
DetailsCompositional bias: {"description":"Basic and acidic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues49
DetailsZinc finger: {"description":"PHD-type 1","evidences":[{"source":"PROSITE-ProRule","id":"PRU00146","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues58
DetailsZinc finger: {"description":"PHD-type 2; atypical","evidences":[{"source":"PROSITE-ProRule","id":"PRU00146","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues2
DetailsModified residue: {"description":"N6-methylated lysine; alternate","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues2
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues4
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84244","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues2
DetailsModified residue: {"description":"N6-methylated lysine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues2
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues2
DetailsModified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues2
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI16
Number of Residues4
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI17
Number of Residues4
DetailsModified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI18
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine; by PAK2","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI19
Number of Residues4
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI20
Number of Residues2
DetailsModified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI21
Number of Residues2
DetailsModified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI22
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI23
Number of Residues4
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI24
Number of Residues2
DetailsModified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine; alternate","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI25
Number of Residues4
DetailsModified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI26
Number of Residues2
DetailsModified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI27
Number of Residues2
DetailsModified residue: {"description":"N5-methylglutamine","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI28
Number of Residues2
DetailsModified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI29
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI30
Number of Residues2
DetailsGlycosylation: {"description":"O-linked (GlcNAc) serine","evidences":[{"source":"UniProtKB","id":"P62807","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI31
Number of Residues4
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"UniProtKB","id":"P0C1H4","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

238895

PDB entries from 2025-07-16

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