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- PDB-7yi2: Cryo-EM structure of Rpd3S in loose-state Rpd3S-NCP complex -

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Basic information

Entry
Database: PDB / ID: 7yi2
TitleCryo-EM structure of Rpd3S in loose-state Rpd3S-NCP complex
Components
  • (Transcriptional regulatory protein ...) x 2
  • (Wisdom 601 DNA (167- ...) x 2
  • Chromatin modification-related protein EAF3
  • Histone deacetylase RPD3
KeywordsGENE REGULATION / Dynamic Histone Modifications / Histone Deacetylase Complex
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 / regulation of RNA stability / nucleophagy / HDACs deacetylate histones / DNA replication-dependent chromatin assembly / histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / histone H3K4 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / histone H4K12 deacetylase activity, hydrolytic mechanism / histone deacetylase / histone H3K9 deacetylase activity, hydrolytic mechanism / 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 / NuA4 histone acetyltransferase complex / Sin3-type complex / Estrogen-dependent gene expression / positive regulation of macroautophagy / histone deacetylase complex / histone acetyltransferase complex / : / nuclear periphery / histone reader activity / meiotic cell cycle / positive regulation of transcription elongation by RNA polymerase II / transcription elongation by RNA polymerase II / double-strand break repair via nonhomologous end joining / G1/S transition of mitotic cell cycle / transcription corepressor activity / G2/M transition of mitotic cell cycle / 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 / Histone deacetylase domain / Chromo/chromo shadow domain / Chromatin organization modifier domain / Arginase; Chain A / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Transcriptional regulatory protein SIN3 / Histone deacetylase RPD3 / Transcriptional regulatory protein RCO1 / Chromatin modification-related protein EAF3
Similarity search - Component
Biological speciessynthetic construct (others)
Saccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLi, H.T. / Yan, C.Y. / Guan, H.P. / Wang, P.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31725014 China
National Natural Science Foundation of China (NSFC)91753203 China
Ministry of Science and Technology (MoST, China)2020YFA0803300 China
Ministry of Science and Technology (MoST, China)2021YFA1300100 China
CitationJournal: Nature / Year: 2023
Title: Diverse modes of H3K36me3-guided nucleosomal deacetylation by Rpd3S.
Authors: Haipeng Guan / Pei Wang / Pei Zhang / Chun Ruan / Yutian Ou / Bo Peng / Xiangdong Zheng / Jianlin Lei / Bing Li / Chuangye Yan / Haitao Li /
Abstract: Context-dependent dynamic histone modifications constitute a key epigenetic mechanism in gene regulation. The Rpd3 small (Rpd3S) complex recognizes histone H3 trimethylation on lysine 36 (H3K36me3) ...Context-dependent dynamic histone modifications constitute a key epigenetic mechanism in gene regulation. The Rpd3 small (Rpd3S) complex recognizes histone H3 trimethylation on lysine 36 (H3K36me3) and deacetylates histones H3 and H4 at multiple sites across transcribed regions. Here we solved the cryo-electron microscopy structures of Saccharomyces cerevisiae Rpd3S in its free and H3K36me3 nucleosome-bound states. We demonstrated a unique architecture of Rpd3S, in which two copies of Eaf3-Rco1 heterodimers are asymmetrically assembled with Rpd3 and Sin3 to form a catalytic core complex. Multivalent recognition of two H3K36me3 marks, nucleosomal DNA and linker DNAs by Eaf3, Sin3 and Rco1 positions the catalytic centre of Rpd3 next to the histone H4 N-terminal tail for deacetylation. In an alternative catalytic mode, combinatorial readout of unmethylated histone H3 lysine 4 and H3K36me3 by Rco1 and Eaf3 directs histone H3-specific deacetylation except for the registered histone H3 acetylated lysine 9. Collectively, our work illustrates dynamic and diverse modes of multivalent nucleosomal engagement and methylation-guided deacetylation by Rpd3S, highlighting the exquisite complexity of epigenetic regulation with delicately designed multi-subunit enzymatic machineries in transcription and beyond.
History
DepositionJul 14, 2022Deposition site: PDBJ / Processing site: PDBJ
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Wisdom 601 DNA (167-MER)
H: Wisdom 601 DNA (167-MER)
A: Transcriptional regulatory protein SIN3
B: Histone deacetylase RPD3
C: Chromatin modification-related protein EAF3
D: Transcriptional regulatory protein RCO1
E: Transcriptional regulatory protein RCO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)530,61212
Polymers530,2857
Non-polymers3275
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Wisdom 601 DNA (167- ... , 2 types, 2 molecules GH

#1: DNA chain Wisdom 601 DNA (167-MER)


Mass: 51308.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#2: DNA chain Wisdom 601 DNA (167-MER)


Mass: 51798.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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

#3: Protein Transcriptional regulatory protein SIN3


Mass: 175047.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: SIN3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P22579
#6: Protein Transcriptional regulatory protein RCO1


Mass: 78951.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: RCO1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q04779

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Protein , 2 types, 2 molecules BC

#4: Protein Histone deacetylase RPD3


Mass: 48961.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P32561
#5: Protein Chromatin modification-related protein EAF3 / ESA1-associated factor 3


Mass: 45266.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: EAF3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q12432

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Non-polymers , 1 types, 5 molecules

#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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

Component
IDNameTypeEntity IDParent-IDSource
1Rpd3S complex with H3K36me3 nucleosomeCOMPLEX#1-#60RECOMBINANT
2DNACOMPLEX#1-#21RECOMBINANT
3SIN3/RPD3/EAF3/RCO1COMPLEX#3-#61RECOMBINANT
Molecular weightValue: 723 kDa/nm / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21synthetic construct (others)32630
32Saccharomyces cerevisiae S288C (yeast)559292
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21synthetic construct (others)32630
32Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 7.5
SpecimenConc.: 0.7 mg/ml / Embedding 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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 1800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 89653 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00312469
ELECTRON MICROSCOPYf_angle_d0.54916949
ELECTRON MICROSCOPYf_dihedral_angle_d16.4351840
ELECTRON MICROSCOPYf_chiral_restr0.0391826
ELECTRON MICROSCOPYf_plane_restr0.0062046

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