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- EMDB-37096: Rpd3S histone deacetylase complex -

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Basic information

Entry
Database: EMDB / ID: EMD-37096
TitleRpd3S histone deacetylase complex
Map data
Sample
  • Complex: Histone deacetylase complex Rpd3S in its apo form
    • Protein or peptide: Histone deacetylase RPD3
    • Protein or peptide: Transcriptional regulatory protein SIN3
    • Protein or peptide: Chromatin modification-related protein EAF3
    • Protein or peptide: Transcriptional regulatory protein RCO1
KeywordsRpd3S / HDAC / Hho1 / cryptic transcription / TRANSCRIPTION
Function / homology
Function and homology information


nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Snt2C complex / negative regulation of silent mating-type cassette heterochromatin formation / negative regulation of reciprocal meiotic recombination / Rpd3L complex / protein localization to nucleolar rDNA repeats / negative regulation of rDNA heterochromatin formation / Rpd3L-Expanded complex / Rpd3S complex ...nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Snt2C complex / negative regulation of silent mating-type cassette heterochromatin formation / negative regulation of reciprocal meiotic recombination / Rpd3L complex / protein localization to nucleolar rDNA repeats / negative regulation of rDNA heterochromatin formation / Rpd3L-Expanded complex / Rpd3S complex / rDNA chromatin condensation / nucleophagy / regulation of RNA stability / HDACs deacetylate histones / histone deacetylase activity, hydrolytic mechanism / DNA replication-dependent chromatin assembly / histone deacetylase / nucleosome disassembly / SUMOylation of chromatin organization proteins / cellular response to nitrogen starvation / regulation of DNA-templated DNA replication initiation / negative regulation of transcription by RNA polymerase I / histone deacetylase activity / Sin3-type complex / NuA4 histone acetyltransferase complex / : / histone reader activity / histone deacetylase complex / Estrogen-dependent gene expression / positive regulation of macroautophagy / histone acetyltransferase complex / nuclear periphery / meiotic cell cycle / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / G1/S transition of mitotic cell cycle / double-strand break repair via nonhomologous end joining / G2/M transition of mitotic cell cycle / transcription corepressor activity / heterochromatin formation / nucleosome assembly / cellular response to heat / response to oxidative stress / transcription coactivator activity / cell division / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
: / : / MSL3 chromodomain-like / Histone deacetylase interacting domain / Sin3, C-terminal / Transcriptional regulatory protein Sin3-like / Sin3 family co-repressor / C-terminal domain of Sin3a protein / Histone deacetylase (HDAC) interacting / Paired amphipathic helix ...: / : / MSL3 chromodomain-like / Histone deacetylase interacting domain / Sin3, C-terminal / Transcriptional regulatory protein Sin3-like / Sin3 family co-repressor / C-terminal domain of Sin3a protein / Histone deacetylase (HDAC) interacting / Paired amphipathic helix / Paired amphipathic helix superfamily / Paired amphipathic helix repeat / PAH domain profile. / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / Histone deacetylase / Chromo/chromo shadow domain / Chromatin organization modifier domain / : / Chromo-like domain superfamily / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Transcriptional regulatory protein SIN3 / Histone deacetylase RPD3 / Transcriptional regulatory protein RCO1 / Chromatin modification-related protein EAF3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsDong S / Li H / Wang M / Rasheed N / Zou B / Gao X / Guan J / Li W / Zhang J / Wang C ...Dong S / Li H / Wang M / Rasheed N / Zou B / Gao X / Guan J / Li W / Zhang J / Wang C / Zhou N / Shi X / Li M / Zhou M / Huang J / Zhang Y / Wong KH / Zhang X / Chao WCH / Jun H
Funding support China, 8 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)NSFC U20A2013 China
National Natural Science Foundation of China (NSFC)32241021 China
National Natural Science Foundation of China (NSFC)32170189 China
Other governmentMYRG2018-00221-FHS
Other government0009/2018/A1
Other government0032/2021/A1
Other government202102080156
Other government2019QN01Y051
CitationJournal: Cell Res / Year: 2023
Title: Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex.
Authors: Shuqi Dong / Huadong Li / Meilin Wang / Nadia Rasheed / Binqian Zou / Xijie Gao / Jiali Guan / Weijie Li / Jiale Zhang / Chi Wang / Ningkun Zhou / Xue Shi / Mei Li / Min Zhou / Junfeng Huang ...Authors: Shuqi Dong / Huadong Li / Meilin Wang / Nadia Rasheed / Binqian Zou / Xijie Gao / Jiali Guan / Weijie Li / Jiale Zhang / Chi Wang / Ningkun Zhou / Xue Shi / Mei Li / Min Zhou / Junfeng Huang / He Li / Ying Zhang / Koon Ho Wong / Xiaofei Zhang / William Chong Hang Chao / Jun He /
Abstract: In Saccharomyces cerevisiae, cryptic transcription at the coding region is prevented by the activity of Sin3 histone deacetylase (HDAC) complex Rpd3S, which is carried by the transcribing RNA ...In Saccharomyces cerevisiae, cryptic transcription at the coding region is prevented by the activity of Sin3 histone deacetylase (HDAC) complex Rpd3S, which is carried by the transcribing RNA polymerase II (RNAPII) to deacetylate and stabilize chromatin. Despite its fundamental importance, the mechanisms by which Rpd3S deacetylates nucleosomes and regulates chromatin dynamics remain elusive. Here, we determined several cryo-EM structures of Rpd3S in complex with nucleosome core particles (NCPs), including the H3/H4 deacetylation states, the alternative deacetylation state, the linker tightening state, and a state in which Rpd3S co-exists with the Hho1 linker histone on NCP. These structures suggest that Rpd3S utilizes a conserved Sin3 basic surface to navigate through the nucleosomal DNA, guided by its interactions with H3K36 methylation and the extra-nucleosomal DNA linkers, to target acetylated H3K9 and sample other histone tails. Furthermore, our structures illustrate that Rpd3S reconfigures the DNA linkers and acts in concert with Hho1 to engage the NCP, potentially unraveling how Rpd3S and Hho1 work in tandem for gene silencing.
History
DepositionAug 6, 2023-
Header (metadata) releaseSep 13, 2023-
Map releaseSep 13, 2023-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37096.png

Downloads & links

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Map

FileDownload / File: emd_37096.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 330 pix.
= 290.4 Å		0.88 Å/pix.
x 330 pix.
= 290.4 Å		0.88 Å/pix.
x 330 pix.
= 290.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.233
Minimum - Maximum-0.30312526 - 0.8124601
Average (Standard dev.)0.0033835904 (±0.0318527)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 290.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37096_msk_1.map
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Half map: #2

Fileemd_37096_half_map_1.map
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Half map: #1

Fileemd_37096_half_map_2.map
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Sample components

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Entire : Histone deacetylase complex Rpd3S in its apo form

EntireName: Histone deacetylase complex Rpd3S in its apo form
Components
  • Complex: Histone deacetylase complex Rpd3S in its apo form
    • Protein or peptide: Histone deacetylase RPD3
    • Protein or peptide: Transcriptional regulatory protein SIN3
    • Protein or peptide: Chromatin modification-related protein EAF3
    • Protein or peptide: Transcriptional regulatory protein RCO1

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Supramolecule #1: Histone deacetylase complex Rpd3S in its apo form

SupramoleculeName: Histone deacetylase complex Rpd3S in its apo form / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 527.7 KDa

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Macromolecule #1: Histone deacetylase RPD3

MacromoleculeName: Histone deacetylase RPD3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone deacetylase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 48.961957 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVYEATPFDP ITVKPSDKRR VAYFYDADVG NYAYGAGHPM KPHRIRMAHS LIMNYGLYKK MEIYRAKPAT KQEMCQFHTD EYIDFLSRV TPDNLEMFKR ESVKFNVGDD CPVFDGLYEY CSISGGGSME GAARLNRGKC DVAVNYAGGL HHAKKSEASG F CYLNDIVL ...String:
MVYEATPFDP ITVKPSDKRR VAYFYDADVG NYAYGAGHPM KPHRIRMAHS LIMNYGLYKK MEIYRAKPAT KQEMCQFHTD EYIDFLSRV TPDNLEMFKR ESVKFNVGDD CPVFDGLYEY CSISGGGSME GAARLNRGKC DVAVNYAGGL HHAKKSEASG F CYLNDIVL GIIELLRYHP RVLYIDIDVH HGDGVEEAFY TTDRVMTCSF HKYGEFFPGT GELRDIGVGA GKNYAVNVPL RD GIDDATY RSVFEPVIKK IMEWYQPSAV VLQCGGDSLS GDRLGCFNLS MEGHANCVNY VKSFGIPMMV VGGGGYTMRN VAR TWCFET GLLNNVVLDK DLPYNEYYEY YGPDYKLSVR PSNMFNVNTP EYLDKVMTNI FANLENTKYA PSVQLNHTPR DAED LGDVE EDSAEAKDTK GGSQYARDLH VEHDNEFY

UniProtKB: Histone deacetylase RPD3

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Macromolecule #2: Transcriptional regulatory protein SIN3

MacromoleculeName: Transcriptional regulatory protein SIN3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 157.586844 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHHHP QLAMWSHPQF EKGGGSGGGS GGGSWSHPQF EKENLYFQSD YRPLNVKDAL SYLEQVKFQF SSRPDIYNLF LDIMKDFKS QAIDTPGVIE RVSTLFRGYP ILIQGFNTFL PQGYRIECSS NPDDPIRVTT PMGTTTVNNN ISPSGRGTTD A QELGSFPE ...String:
MHHHHHHHHP QLAMWSHPQF EKGGGSGGGS GGGSWSHPQF EKENLYFQSD YRPLNVKDAL SYLEQVKFQF SSRPDIYNLF LDIMKDFKS QAIDTPGVIE RVSTLFRGYP ILIQGFNTFL PQGYRIECSS NPDDPIRVTT PMGTTTVNNN ISPSGRGTTD A QELGSFPE SDGNGVQQPS NVPMVPSSVY QSEQNQDQQQ SLPLLATSSG LPSIQQPEMP AHRQIPQSQS LVPQEDAKKN VD VEFSQAI SYVNKIKTRF ADQPDIYKHF LEILQTYQRE QKPINEVYAQ VTHLFQNAPD LLEDFKKFLP DSSASANQQV QHA QQHAQQ QHEAQMHAQA QAQAQAQAQV EQQKQQQQFL YPASGYYGHP SNRGIPQQNL PPIGSFSPPT NGSTVHEAYQ DQQH MQPPH FMPLPSIVQH GPNMVHQGIA NENPPLSDLR TSLTEQYAPS SIQHQQQHPQ SISPIANTQY GDIPVRPEID LDPSI VPVV PEPTEPIENN ISLNEEVTFF EKAKRYIGNK HLYTEFLKIL NLYSQDILDL DDLVEKVDFY LGSNKELFTW FKNFVG YQE KTKCIENIVH EKHRLDLDLC EAFGPSYKRL PKSDTFMPCS GRDDMCWEVL NDEWVGHPVW ASEDSGFIAH RKNQYEE TL FKIEEERHEY DFYIESNLRT IQCLETIVNK IENMTENEKA NFKLPPGLGH TSMTIYKKVI RKVYDKERGF EIIDALHE H PAVTAPVVLK RLKQKDEEWR RAQREWNKVW RELEQKVFFK SLDHLGLTFK QADKKLLTTK QLISEISSIK VDQTNKKIH WLTPKPKSQL DFDFPDKNIF YDILCLADTF ITHTTAYSNP DKERLKDLLK YFISLFFSIS FEKIEESLYS HKQNVSESSG SDDGSSIAS RKRPYQQEMS LLDILHRSRY QKLKRSNDED GKVPQLSEPP EEEPNTIEEE ELIDEEAKNP WLTGNLVEEA N SQGIIQNR SIFNLFANTN IYIFFRHWTT IYERLLEIKQ MNERVTKEIN TRSTVTFAKD LDLLSSQLSE MGLDFVGEDA YK QVLRLSR RLINGDLEHQ WFEESLRQAY NNKAFKLYTI DKVTQSLVKH AHTLMTDAKT AEIMALFVKD RNASTTSAKD QII YRLQVR SHMSNTENMF RIEFDKRTLH VSIQYIALDD LTLKEPKADE DKWKYYVTSY ALPHPTEGIP HEKLKIPFLE RLIE FGQDI DGTEVDEEFS PEGISVSTLK IKIQPITYQL HIENGSYDVF TRKATNKYPT IANDNTQKGM VSQKKELISK FLDCA VGLR NNLDEAQKLS MQKKWENLKD SIAKTSAGNQ GIESETEKGK ITKQEQSDNL DSSTASVLPA SITTVPQDDN IETTGN TES SDKGAKIQ

UniProtKB: Transcriptional regulatory protein SIN3

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Macromolecule #3: Chromatin modification-related protein EAF3

MacromoleculeName: Chromatin modification-related protein EAF3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 45.266406 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVDLEQEFAL GGRCLAFHGP LMYEAKILKI WDPSSKMYTS IPNDKPGGSS QATKEIKPQK LGEDESIPEE IINGKCFFIH YQGWKSSWD EWVGYDRIRA YNEENIAMKK RLANEAKEAK KSLLEQQKKK KLSTSLGGPS NGGKRKGDSR SNASISKSTS Q SFLTSSVS ...String:
MVDLEQEFAL GGRCLAFHGP LMYEAKILKI WDPSSKMYTS IPNDKPGGSS QATKEIKPQK LGEDESIPEE IINGKCFFIH YQGWKSSWD EWVGYDRIRA YNEENIAMKK RLANEAKEAK KSLLEQQKKK KLSTSLGGPS NGGKRKGDSR SNASISKSTS Q SFLTSSVS GRKSGRSSAN SLHPGSSLRS SSDQNGNDDR RRSSSLSPNM LHHIAGYPTP KISLQIPIKL KSVLVDDWEY VT KDKKICR LPADVTVEMV LNKYEHEVSQ ELESPGSQSQ LSEYCAGLKL YFDKCLGNML LYRLERLQYD ELLKKSSKDQ KPL VPIRIY GAIHLLRLIS VLPELISSTT MDLQSCQLLI KQTEDFLVWL LMHVDEYFND KDPNRSDDAL YVNTSSQYEG VALG M

UniProtKB: Chromatin modification-related protein EAF3

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Macromolecule #4: Transcriptional regulatory protein RCO1

MacromoleculeName: Transcriptional regulatory protein RCO1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 84.469328 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDTSKKDTTR SPSHSNSSSP SSSSLSSSSS KEKKRPKRLS SQNVNYDLKR RKIITSEGIE RSFKNEHSNL AVEDNIPEEE PKELLEKDS KGNIIKLNEP STISEDSKVS VTGLPLNKGP SEKIKRESLW NYRKNLGGQS NNSEMTLVPS KRFTQVPKNF Q DLNRNDLK ...String:
MDTSKKDTTR SPSHSNSSSP SSSSLSSSSS KEKKRPKRLS SQNVNYDLKR RKIITSEGIE RSFKNEHSNL AVEDNIPEEE PKELLEKDS KGNIIKLNEP STISEDSKVS VTGLPLNKGP SEKIKRESLW NYRKNLGGQS NNSEMTLVPS KRFTQVPKNF Q DLNRNDLK TFLTENMTEE SNIRSTIGWN GDIINRTRDR EPESDRDNKK LSNIRTKIIL STNATYDSKS KLFGQNSIKS TS NASEKIF RDKNNSTIDF ENEDFCSACN QSGSFLCCDT CPKSFHFLCL DPPIDPNNLP KGDWHCNECK FKIFINNSMA TLK KIESNF IKQNNNVKIF AKLLFNIDSH NPKQFQLPNY IKETFPAVKT GSRGQYSDEN DKIPLTDRQL FNTSYGQSIT KLDS YNPDT HIDSNSGKFL ICYKCNQTRL GSWSHPENSR LIMTCDYCQT PWHLDCVPRA SFKNLGSKWK CPLHSPTKVY KKIHH CQED NSVNYKVWKK QRLINKKNQL YYEPLQKIGY QNNGNIQIIP TTSHTDYDFN QDFKITQIDE NSIKYDFFDK IYKSKM VQK RKLFQFQESL IDKLVSNGSQ NGNSEDNMVK DIASLIYFQV SNNDKSSNNK SASKSNNLRK LWDLKELTNV VVPNELD SI QFNDFSSDEI KHLLYLKKII ESKPKEELLK FLNIENPENQ SEMHHHHHHH HPQLAMWSHP QFEKGGGSGG GSGGGSWS H PQFEKENLYF QS

UniProtKB: Transcriptional regulatory protein RCO1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

Concentration0.7 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 287163
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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