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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

8HXY

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

Functional Information from GO Data
ChainGOidnamespacecontents
A0000786cellular_componentnucleosome
A0003677molecular_functionDNA binding
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
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
E0005515molecular_functionprotein binding
E0005634cellular_componentnucleus
E0005654cellular_componentnucleoplasm
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
K0000086biological_processG2/M transition of mitotic cell cycle
K0000122biological_processnegative regulation of transcription by RNA polymerase II
K0000785cellular_componentchromatin
K0003713molecular_functiontranscription coactivator activity
K0003714molecular_functiontranscription corepressor activity
K0005515molecular_functionprotein binding
K0005634cellular_componentnucleus
K0006303biological_processdouble-strand break repair via nonhomologous end joining
K0006325biological_processchromatin organization
K0006334biological_processnucleosome assembly
K0006355biological_processregulation of DNA-templated transcription
K0006357biological_processregulation of transcription by RNA polymerase II
K0010558biological_processnegative regulation of macromolecule biosynthetic process
K0010628biological_processpositive regulation of gene expression
K0016479biological_processnegative regulation of transcription by RNA polymerase I
K0030174biological_processregulation of DNA-templated DNA replication initiation
K0032221cellular_componentRpd3S complex
K0033698cellular_componentRpd3L complex
K0034605biological_processcellular response to heat
K0042802molecular_functionidentical protein binding
K0044804biological_processnucleophagy
K0045944biological_processpositive regulation of transcription by RNA polymerase II
K0051301biological_processcell division
K0051321biological_processmeiotic cell cycle
K0061186biological_processnegative regulation of silent mating-type cassette heterochromatin formation
K0061188biological_processnegative regulation of rDNA heterochromatin formation
K0070210cellular_componentRpd3L-Expanded complex
K0070550biological_processrDNA chromatin condensation
K0070822cellular_componentSin3-type complex
L0000082biological_processG1/S transition of mitotic cell cycle
L0000086biological_processG2/M transition of mitotic cell cycle
L0000118cellular_componenthistone deacetylase complex
L0000122biological_processnegative regulation of transcription by RNA polymerase II
L0003713molecular_functiontranscription coactivator activity
L0003714molecular_functiontranscription corepressor activity
L0004407molecular_functionhistone deacetylase activity
L0005515molecular_functionprotein binding
L0005634cellular_componentnucleus
L0005737cellular_componentcytoplasm
L0006325biological_processchromatin organization
L0006334biological_processnucleosome assembly
L0006355biological_processregulation of DNA-templated transcription
L0006357biological_processregulation of transcription by RNA polymerase II
L0006368biological_processtranscription elongation by RNA polymerase II
L0006979biological_processresponse to oxidative stress
L0006995biological_processcellular response to nitrogen starvation
L0008270molecular_functionzinc ion binding
L0010557biological_processpositive regulation of macromolecule biosynthetic process
L0016239biological_processpositive regulation of macroautophagy
L0016479biological_processnegative regulation of transcription by RNA polymerase I
L0016787molecular_functionhydrolase activity
L0030174biological_processregulation of DNA-templated DNA replication initiation
L0031507biological_processheterochromatin formation
L0032221cellular_componentRpd3S complex
L0033698cellular_componentRpd3L complex
L0034399cellular_componentnuclear periphery
L0034503biological_processprotein localization to nucleolar rDNA repeats
L0034605biological_processcellular response to heat
L0044804biological_processnucleophagy
L0045128biological_processnegative regulation of reciprocal meiotic recombination
L0045944biological_processpositive regulation of transcription by RNA polymerase II
L0051321biological_processmeiotic cell cycle
L0061186biological_processnegative regulation of silent mating-type cassette heterochromatin formation
L0061188biological_processnegative regulation of rDNA heterochromatin formation
L0070210cellular_componentRpd3L-Expanded complex
L0070211cellular_componentSnt2C complex
L0070550biological_processrDNA chromatin condensation
L0070822cellular_componentSin3-type complex
L0141221molecular_functionhistone deacetylase activity, hydrolytic mechanism
M0000122biological_processnegative regulation of transcription by RNA polymerase II
M0000123cellular_componenthistone acetyltransferase complex
M0005515molecular_functionprotein binding
M0005634cellular_componentnucleus
M0006281biological_processDNA repair
M0006325biological_processchromatin organization
M0006334biological_processnucleosome assembly
M0006335biological_processDNA replication-dependent chromatin assembly
M0006337biological_processnucleosome disassembly
M0006338biological_processchromatin remodeling
M0006351biological_processDNA-templated transcription
M0006355biological_processregulation of DNA-templated transcription
M0006357biological_processregulation of transcription by RNA polymerase II
M0006368biological_processtranscription elongation by RNA polymerase II
M0006974biological_processDNA damage response
M0030174biological_processregulation of DNA-templated DNA replication initiation
M0032221cellular_componentRpd3S complex
M0032968biological_processpositive regulation of transcription elongation by RNA polymerase II
M0035267cellular_componentNuA4 histone acetyltransferase complex
M0043487biological_processregulation of RNA stability
M0045892biological_processnegative regulation of DNA-templated transcription
M0060195biological_processnegative regulation of antisense RNA transcription
M0140003molecular_functionhistone H3K36me3 reader activity
M0140566molecular_functionhistone reader activity
M1990453cellular_componentnucleosome disassembly/reassembly complex
N0000118cellular_componenthistone deacetylase complex
N0000122biological_processnegative regulation of transcription by RNA polymerase II
N0005634cellular_componentnucleus
N0006325biological_processchromatin organization
N0006334biological_processnucleosome assembly
N0006357biological_processregulation of transcription by RNA polymerase II
N0006368biological_processtranscription elongation by RNA polymerase II
N0008270molecular_functionzinc ion binding
N0030174biological_processregulation of DNA-templated DNA replication initiation
N0032221cellular_componentRpd3S complex
N0045944biological_processpositive regulation of transcription by RNA polymerase II
N0046872molecular_functionmetal ion binding
N0060195biological_processnegative regulation of antisense RNA transcription
P0000118cellular_componenthistone deacetylase complex
P0000122biological_processnegative regulation of transcription by RNA polymerase II
P0005634cellular_componentnucleus
P0006325biological_processchromatin organization
P0006334biological_processnucleosome assembly
P0006357biological_processregulation of transcription by RNA polymerase II
P0006368biological_processtranscription elongation by RNA polymerase II
P0008270molecular_functionzinc ion binding
P0030174biological_processregulation of DNA-templated DNA replication initiation
P0032221cellular_componentRpd3S complex
P0045944biological_processpositive regulation of transcription by RNA polymerase II
P0046872molecular_functionmetal ion binding
P0060195biological_processnegative regulation of antisense RNA transcription
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
NCYS263-CYS306
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues4
DetailsModified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues1
DetailsModified residue: {"description":"Phosphothreonine; by HASPIN and VRK1","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues2
DetailsModified residue: {"description":"N6-methyllysine","evidences":[{"source":"UniProtKB","id":"P68431","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues2
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues4
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84228","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues4
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues2
DetailsModified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues2
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues2
DetailsLipidation: {"description":"S-palmitoyl cysteine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues2
DetailsModified residue: {"description":"Citrulline; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues1
DetailsModified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"12138181","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues1
DetailsModified residue: {"description":"5-glutamyl serotonin; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI15
Number of Residues2
DetailsModified residue: {"description":"Phosphothreonine; by PKC","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI16
Number of Residues1
DetailsModified residue: {"description":"Symmetric dimethylarginine; by PRMT5; alternate","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI17
Number of Residues1
DetailsModified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"12138181","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI18
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine; alternate; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI19
Number of Residues1
DetailsModified residue: {"description":"N6-lactoyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84228","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI21
Number of Residues4
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI22
Number of Residues4
DetailsModified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI23
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine; by PAK2","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI24
Number of Residues4
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI25
Number of Residues2
DetailsModified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI26
Number of Residues2
DetailsModified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI27
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_FI28
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_FI29
Number of Residues2
DetailsModified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine; alternate","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI30
Number of Residues4
DetailsModified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI31
Number of Residues2
DetailsModified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI32
Number of Residues2
DetailsModified residue: {"description":"N5-methylglutamine","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI33
Number of Residues2
DetailsModified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI34
Number of Residues7
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI35
Number of Residues2
DetailsGlycosylation: {"description":"O-linked (GlcNAc) serine","evidences":[{"source":"UniProtKB","id":"P62807","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI36
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
site_idSWS_FT_FI37
Number of Residues312
DetailsRegion: {"description":"Histone deacetylase"}
ChainResidueDetails
site_idSWS_FT_FI38
Number of Residues20
DetailsMotif: {"description":"ESA1-RPD3 motif"}
ChainResidueDetails
site_idSWS_FT_FI39
Number of Residues1
DetailsActive site: {"evidences":[{"evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI40
Number of Residues9
DetailsCompositional bias: {"description":"Basic and acidic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}
ChainResidueDetails
site_idSWS_FT_FI41
Number of Residues49
DetailsZinc finger: {"description":"PHD-type 1","evidences":[{"source":"PROSITE-ProRule","id":"PRU00146","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI42
Number of Residues58
DetailsZinc finger: {"description":"PHD-type 2; atypical","evidences":[{"source":"PROSITE-ProRule","id":"PRU00146","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

239492

PDB entries from 2025-07-30

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