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- PDB-8w9c: Cryo-EM structure of the Rpd3S complex from budding yeast -

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Basic information

Entry
Database: PDB / ID: 8w9c
TitleCryo-EM structure of the Rpd3S complex from budding yeast
Components
  • (Transcriptional regulatory protein ...) x 2
  • Chromatin modification-related protein EAF3
  • Histone deacetylase RPD3
KeywordsDNA BINDING PROTEIN / Rpd3S / HDAC / Sin3 / Rpd3
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 / cellular response to nitrogen starvation / SUMOylation of chromatin organization proteins / 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 / Estrogen-dependent gene expression / histone deacetylase complex / 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 (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWang, C. / Zhan, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci Adv / Year: 2024
Title: Structures and dynamics of Rpd3S complex bound to nucleosome.
Authors: Chengcheng Wang / Chen Chu / Zhouyan Guo / Xiechao Zhan /
Abstract: The Rpd3S complex plays a pivotal role in facilitating local histone deacetylation in the transcribed regions to suppress intragenic transcription initiation. Here, we present the cryo-electron ...The Rpd3S complex plays a pivotal role in facilitating local histone deacetylation in the transcribed regions to suppress intragenic transcription initiation. Here, we present the cryo-electron microscopy structures of the budding yeast Rpd3S complex in both its apo and three nucleosome-bound states at atomic resolutions, revealing the exquisite architecture of Rpd3S to well accommodate a mononucleosome without linker DNA. The Rpd3S core, containing a Sin3 Lobe and two NB modules, is a rigid complex and provides three positive-charged anchors (Sin3_HCR and two Rco1_NIDs) to connect nucleosomal DNA. In three nucleosome-bound states, the Rpd3S core exhibits three distinct orientations relative to the nucleosome, assisting the sector-shaped deacetylase Rpd3 to locate above the SHL5-6, SHL0-1, or SHL2-3, respectively. Our work provides a structural framework that reveals a dynamic working model for the Rpd3S complex to engage diverse deacetylation sites.
History
DepositionSep 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulatory protein SIN3
E: Transcriptional regulatory protein RCO1
B: Histone deacetylase RPD3
C: Chromatin modification-related protein EAF3
D: Chromatin modification-related protein EAF3
F: Transcriptional regulatory protein RCO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)472,98115
Polymers472,4456
Non-polymers5369
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Transcriptional regulatory protein ... , 2 types, 3 molecules AEF

#1: Protein Transcriptional regulatory protein SIN3


Mass: 175047.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22579
#2: Protein Transcriptional regulatory protein RCO1


Mass: 78951.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04779

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Protein , 2 types, 3 molecules BCD

#3: Protein Histone deacetylase RPD3


Mass: 48961.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32561
#4: Protein Chromatin modification-related protein EAF3 / ESA1-associated factor 3


Mass: 45266.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12432

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Non-polymers , 2 types, 9 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The Rpd3S complex / Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 1700 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 378011 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01415383
ELECTRON MICROSCOPYf_angle_d0.6520761
ELECTRON MICROSCOPYf_dihedral_angle_d11.5521994
ELECTRON MICROSCOPYf_chiral_restr0.042242
ELECTRON MICROSCOPYf_plane_restr0.0052655

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