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- EMDB-35450: Cryo-EM structure of the Rpd3S core complex -

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Basic information

Entry
Database: EMDB / ID: EMD-35450
TitleCryo-EM structure of the Rpd3S core complex
Map data
Sample
  • Complex: Eaf3 CHD domain bound to the nucleosome
    • Protein or peptide: Histone H3
    • Protein or peptide: Transcriptional regulatory protein SIN3
    • Protein or peptide: Histone deacetylase RPD3
    • Protein or peptide: RCO1 isoform 1
    • Protein or peptide: Chromatin modification-related protein EAF3
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
KeywordsHDAC / TRANSCRIPTION
Function / homology
Function and homology information


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 ...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 / HDACs deacetylate histones / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / SUMOylation of chromatin organization proteins / cellular response to nitrogen starvation / regulation of DNA-templated DNA replication initiation / histone deacetylase activity / negative regulation of transcription by RNA polymerase I / Sin3-type complex / NuA4 histone acetyltransferase complex / histone deacetylase complex / Estrogen-dependent gene expression / positive regulation of macroautophagy / nuclear periphery / meiotic cell cycle / 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 / structural constituent of chromatin / transcription corepressor activity / nucleosome / heterochromatin formation / nucleosome assembly / cellular response to heat / response to oxidative stress / transcription coactivator activity / chromatin remodeling / protein heterodimerization activity / cell division / DNA repair / 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 / DNA binding / metal ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
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. ...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. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H3 / RCO1 isoform 1 / Chromatin modification-related protein EAF3 / Transcriptional regulatory protein SIN3 / Histone deacetylase RPD3
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / Saccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsZhang Y / Gang C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Res / Year: 2023
Title: Structural basis for nucleosome binding and catalysis by the yeast Rpd3S/HDAC holoenzyme.
Authors: Yueyue Zhang / Mengxue Xu / Po Wang / Jiahui Zhou / Guangxian Wang / Shuailong Han / Gang Cai / Xuejuan Wang /
History
DepositionFeb 23, 2023-
Header (metadata) releaseMar 20, 2024-
Map releaseMar 20, 2024-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35450.png

Downloads & links

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Map

FileDownload / File: emd_35450.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 336 pix.
= 359.52 Å		1.07 Å/pix.
x 336 pix.
= 359.52 Å		1.07 Å/pix.
x 336 pix.
= 359.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.31
Minimum - Maximum-1.4067105 - 2.8095012
Average (Standard dev.)0.0030917174 (±0.06326899)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 359.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35450_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35450_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Eaf3 CHD domain bound to the nucleosome

EntireName: Eaf3 CHD domain bound to the nucleosome
Components
  • Complex: Eaf3 CHD domain bound to the nucleosome
    • Protein or peptide: Histone H3
    • Protein or peptide: Transcriptional regulatory protein SIN3
    • Protein or peptide: Histone deacetylase RPD3
    • Protein or peptide: RCO1 isoform 1
    • Protein or peptide: Chromatin modification-related protein EAF3
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION

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Supramolecule #1: Eaf3 CHD domain bound to the nucleosome

SupramoleculeName: Eaf3 CHD domain bound to the nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 2.563012 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKA

UniProtKB: Histone H3

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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 (brewer's yeast)
Molecular weightTheoretical: 175.047266 KDa
SequenceString: MSQVWHNSNS QSNDVATSND ATGSNERNEK EPSLQGNKPG FVQQQQRITL PSLSALSTKE EDRRDSNGQQ ALTSHAAHIL GYPPPHSNA MPSIATDSAL KQPHEYHPRP KSSSSSPSIN ASLMNAGPAP LPTVGAASFS LSRFDNPLPI KAPVHTEEPK S YNGLQEEE ...String:
MSQVWHNSNS QSNDVATSND ATGSNERNEK EPSLQGNKPG FVQQQQRITL PSLSALSTKE EDRRDSNGQQ ALTSHAAHIL GYPPPHSNA MPSIATDSAL KQPHEYHPRP KSSSSSPSIN ASLMNAGPAP LPTVGAASFS LSRFDNPLPI KAPVHTEEPK S YNGLQEEE KATQRPQDCK EVPAGVQPAD APDPSSNHAD ANDDNNNNEN SHDEDADYRP LNVKDALSYL EQVKFQFSSR PD IYNLFLD IMKDFKSQAI DTPGVIERVS TLFRGYPILI QGFNTFLPQG YRIECSSNPD DPIRVTTPMG TTTVNNNISP SGR GTTDAQ ELGSFPESDG NGVQQPSNVP MVPSSVYQSE QNQDQQQSLP LLATSSGLPS IQQPEMPAHR QIPQSQSLVP QEDA KKNVD VEFSQAISYV NKIKTRFADQ PDIYKHFLEI LQTYQREQKP INEVYAQVTH LFQNAPDLLE DFKKFLPDSS ASANQ QVQH AQQHAQQQHE AQMHAQAQAQ AQAQAQVEQQ KQQQQFLYPA SGYYGHPSNR GIPQQNLPPI GSFSPPTNGS TVHEAY QDQ QHMQPPHFMP LPSIVQHGPN MVHQGIANEN PPLSDLRTSL TEQYAPSSIQ HQQQHPQSIS PIANTQYGDI PVRPEID LD PSIVPVVPEP TEPIENNISL NEEVTFFEKA KRYIGNKHLY TEFLKILNLY SQDILDLDDL VEKVDFYLGS NKELFTWF K NFVGYQEKTK CIENIVHEKH RLDLDLCEAF GPSYKRLPKS DTFMPCSGRD DMCWEVLNDE WVGHPVWASE DSGFIAHRK NQYEETLFKI EEERHEYDFY IESNLRTIQC LETIVNKIEN MTENEKANFK LPPGLGHTSM TIYKKVIRKV YDKERGFEII DALHEHPAV TAPVVLKRLK QKDEEWRRAQ REWNKVWREL EQKVFFKSLD HLGLTFKQAD KKLLTTKQLI SEISSIKVDQ T NKKIHWLT PKPKSQLDFD FPDKNIFYDI LCLADTFITH TTAYSNPDKE RLKDLLKYFI SLFFSISFEK IEESLYSHKQ NV SESSGSD DGSSIASRKR PYQQEMSLLD ILHRSRYQKL KRSNDEDGKV PQLSEPPEEE PNTIEEEELI DEEAKNPWLT GNL VEEANS QGIIQNRSIF NLFANTNIYI FFRHWTTIYE RLLEIKQMNE RVTKEINTRS TVTFAKDLDL LSSQLSEMGL DFVG EDAYK QVLRLSRRLI NGDLEHQWFE ESLRQAYNNK AFKLYTIDKV TQSLVKHAHT LMTDAKTAEI MALFVKDRNA STTSA KDQI IYRLQVRSHM SNTENMFRIE FDKRTLHVSI QYIALDDLTL KEPKADEDKW KYYVTSYALP HPTEGIPHEK LKIPFL ERL IEFGQDIDGT EVDEEFSPEG ISVSTLKIKI QPITYQLHIE NGSYDVFTRK ATNKYPTIAN DNTQKGMVSQ KKELISK FL DCAVGLRNNL DEAQKLSMQK KWENLKDSIA KTSAGNQGIE SETEKGKITK QEQSDNLDSS TASVLPASIT TVPQDDNI E TTGNTESSDK GAKIQ

UniProtKB: Transcriptional regulatory protein SIN3

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Macromolecule #3: Histone deacetylase RPD3

MacromoleculeName: Histone deacetylase RPD3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone deacetylase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 48.961957 KDa
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 #4: RCO1 isoform 1

MacromoleculeName: RCO1 isoform 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 78.951305 KDa
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 SE

UniProtKB: RCO1 isoform 1

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Macromolecule #5: Chromatin modification-related protein EAF3

MacromoleculeName: Chromatin modification-related protein EAF3 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 45.266406 KDa
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 #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #7: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.8 µm
Experimental equipment
Model: Titan Krios / 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: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 107252
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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