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- PDB-8hy0: Composite cryo-EM structure of the histone deacetylase complex Rp... -

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Basic information

Entry
Database: PDB / ID: 8hy0
TitleComposite cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome
Components
  • (DNA (352-MER)) x 2
  • Chromatin modification-related protein EAF3
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
  • Histone deacetylase RPD3
  • RCO1 isoform 1
  • Transcriptional regulatory protein SIN3
KeywordsGENE REGULATION / Histone deacetylase complex / nucleosome
Function / homology
Function and homology information


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 / Rpd3S complex / HDACs deacetylate histones / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / rDNA chromatin condensation ...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 / Rpd3S complex / HDACs deacetylate histones / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / rDNA chromatin condensation / nucleophagy / SUMOylation of chromatin organization proteins / histone deacetylase / negative regulation of transcription by RNA polymerase I / regulation of DNA-templated DNA replication initiation / histone deacetylase activity / Sin3-type complex / histone deacetylase complex / positive regulation of macroautophagy / histone acetyltransferase complex / nuclear periphery / transcription elongation by RNA polymerase II / nucleosome assembly / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / transcription corepressor activity / nucleosome / response to oxidative stress / transcription coactivator activity / chromatin remodeling / cell cycle / protein heterodimerization activity / cell division / DNA repair / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / metal ion 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. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H3 / RCO1 isoform 1 / Chromatin modification-related protein EAF3 / Histone H2B / Histone H4 / Transcriptional regulatory protein SIN3 / Histone deacetylase RPD3 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Saccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsCui, H. / Wang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Structure of histone deacetylase complex Rpd3S bound to nucleosome.
Authors: Wulong Li / Hengjun Cui / Zhimin Lu / Haibo Wang /
Abstract: Crosstalk between histone modifications represents a fundamental epigenetic mechanism in gene regulation. During the transcription elongation process, the histone deacetylase complex Rpd3S is ...Crosstalk between histone modifications represents a fundamental epigenetic mechanism in gene regulation. During the transcription elongation process, the histone deacetylase complex Rpd3S is recruited to H3K36-methylated nucleosomes to suppress cryptic transcription initiation. However, how subunits of Rpd3S are assembled and coordinated to recognize nucleosomal substrates and exert their deacetylation function remains unclear. Here we report the structure of Saccharomyces cerevisiae Rpd3S deacetylase bound to H3K36me3-modified nucleosome at 3.1 Å resolution. It shows that Sin3 and Rco1 subunits orchestrate the assembly of the complex and mediate its contact with nucleosome at multiple sites, with the Sin3-DNA interface as a pivotal anchor. The PHD1 domain of Rco1 recognizes the unmodified H3K4 and places the following H3 tail toward the active site of Rpd3, while the chromodomain of Eaf3 subunit recognizes the H3K36me3 mark and contacts both nucleosomal and linker DNA. The second copy of Eaf3-Rco1 is involved in neighboring nucleosome binding. Our work unravels the structural basis of chromatin targeting and deacetylation by the Rpd3S complex.
History
DepositionJan 5, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN
Revision 1.2Oct 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Dec 27, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B
I: DNA (352-MER)
J: DNA (352-MER)
K: Transcriptional regulatory protein SIN3
L: Histone deacetylase RPD3
M: Chromatin modification-related protein EAF3
N: RCO1 isoform 1
O: Chromatin modification-related protein EAF3
P: RCO1 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)798,51923
Polymers798,06116
Non-polymers4587
Water0
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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Protein , 8 types, 14 molecules AEBFCGDHKLMONP

#1: Protein Histone H3 /


Mass: 15331.982 Da / Num. of mol.: 2 / Mutation: C110A
Source method: isolated from a genetically manipulated source
Details: Author stated that Cys110 residues of chain A/E were mutated to Ala due to the preparation of ML3-modified nucleosome.
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC121398065 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A310TTQ1
#2: Protein Histone H4 /


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC121398084 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8J1LTD2
#3: Protein Histone H2A /


Mass: 13978.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: h2ac14.L / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8
#4: Protein Histone H2B /


Mass: 13524.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC108704303 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8J0U496
#7: 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 (brewer's yeast)
Gene: SIN3, CPE1, GAM2, RPD1, SDI1, SDS16, UME4, YOL004W / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P22579
#8: Protein Histone deacetylase RPD3 / Transcriptional regulatory protein RPD3


Mass: 48961.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPD3, MOF6, REC3, SDI2, SDS6, YNL330C, N0305 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32561, histone deacetylase
#9: Protein Chromatin modification-related protein EAF3


Mass: 45266.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EAF3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A8H4F719
#10: Protein RCO1 isoform 1


Mass: 78951.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RCO1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A8H4BXB0

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (352-MER)


Mass: 108340.836 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (352-MER)


Mass: 109079.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 1 types, 7 molecules

#11: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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: Rpd3S histone deacetylase in complex with nucleosome / Type: COMPLEX / Entity ID: #1-#10 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.80 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
Details: 20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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 FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 44 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
2SerialEM3.8 beta8image acquisition
4Warp1.0.7CTF correction
7UCSF ChimeraX1.5model fitting
9PHENIX1.20.1-4487model refinement
13RELION3.1.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81856 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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