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Open data
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Basic information
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Title | Rpd3S histone deacetylase complex | |||||||||||||||||||||||||||
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![]() | Rpd3S / HDAC / Hho1 / cryptic transcription / TRANSCRIPTION | |||||||||||||||||||||||||||
Function / homology | ![]() nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / Rpd3L complex / protein localization to nucleolar rDNA repeats / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / Rpd3S complex ...nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / Rpd3L complex / protein localization to nucleolar rDNA repeats / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / Rpd3S complex / rDNA chromatin condensation / regulation of RNA stability / nucleophagy / HDACs deacetylate histones / DNA replication-dependent chromatin assembly / histone deacetylase / cellular response to nitrogen starvation / SUMOylation of chromatin organization proteins / nucleosome disassembly / regulation of DNA-templated DNA replication initiation / negative regulation of transcription by RNA polymerase I / histone deacetylase activity / NuA4 histone acetyltransferase complex / Sin3-type complex / Estrogen-dependent gene expression / histone deacetylase complex / positive regulation of macroautophagy / histone acetyltransferase complex / meiotic cell cycle / positive regulation of transcription elongation by RNA polymerase II / methylated histone binding / nuclear periphery / transcription elongation by RNA polymerase II / G1/S transition of mitotic cell cycle / heterochromatin formation / G2/M transition of mitotic cell cycle / double-strand break repair via nonhomologous end joining / transcription corepressor activity / nucleosome assembly / cellular response to heat / transcription coactivator activity / response to oxidative stress / cell division / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.46 Å | |||||||||||||||||||||||||||
![]() | Dong 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 | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 68 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.9 KB 21.9 KB | Display Display | ![]() |
Images | ![]() | 28.5 KB | ||
Masks | ![]() | 137.1 MB | ![]() | |
Filedesc metadata | ![]() | 7.7 KB | ||
Others | ![]() ![]() | 127.4 MB 127.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 811.2 KB | Display | ![]() |
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Full document | ![]() | 810.7 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 16.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8kc7MC ![]() 8kd2C ![]() 8kd3C ![]() 8kd4C ![]() 8kd5C ![]() 8kd6C ![]() 8kd7C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.88 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Half map: #2
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-Half map: #1
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Density Histograms |
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Sample components
-Entire : Histone deacetylase complex Rpd3S in its apo form
Entire | Name: Histone deacetylase complex Rpd3S in its apo form |
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Components |
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-Supramolecule #1: Histone deacetylase complex Rpd3S in its apo form
Supramolecule | Name: Histone deacetylase complex Rpd3S in its apo form / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 527.7 KDa |
-Macromolecule #1: Histone deacetylase RPD3
Macromolecule | Name: Histone deacetylase RPD3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone deacetylase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 48.961957 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #2: Transcriptional regulatory protein SIN3
Macromolecule | Name: Transcriptional regulatory protein SIN3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 157.586844 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #3: Chromatin modification-related protein EAF3
Macromolecule | Name: Chromatin modification-related protein EAF3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 45.266406 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #4: Transcriptional regulatory protein RCO1
Macromolecule | Name: Transcriptional regulatory protein RCO1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 84.469328 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | 3D array |
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Sample preparation
Concentration | 0.7 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination 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
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 287163 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |