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- PDB-8hy0: Composite cryo-EM structure of the histone deacetylase complex Rp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hy0 | ||||||
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Title | Composite cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome | ||||||
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![]() | GENE REGULATION / Histone deacetylase complex / nucleosome | ||||||
Function / homology | ![]() 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 / nucleophagy ...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 / nucleophagy / HDACs deacetylate histones / histone deacetylase / 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 / NuA4 histone acetyltransferase complex / Sin3-type complex / Estrogen-dependent gene expression / histone deacetylase complex / positive regulation of macroautophagy / nuclear periphery / meiotic cell cycle / transcription elongation by RNA polymerase II / heterochromatin formation / double-strand break repair via nonhomologous end joining / G1/S transition of mitotic cell cycle / structural constituent of chromatin / transcription corepressor activity / G2/M transition of mitotic cell cycle / nucleosome / 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 / chromatin / 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 / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
![]() | Cui, H. / Wang, H. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 764.6 KB | Display | ![]() |
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PDB format | ![]() | 575 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 35084MC ![]() 8hxxC ![]() 8hxyC ![]() 8hxzC ![]() 8jhoC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 8 types, 14 molecules AEBFCGDHKLMONP
#1: Protein | 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.) ![]() ![]() ![]() #2: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 13978.241 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 13524.752 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #7: Protein | | Mass: 175047.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SIN3, CPE1, GAM2, RPD1, SDI1, SDS16, UME4, YOL004W / Production host: ![]() #8: Protein | | Mass: 48961.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: RPD3, MOF6, REC3, SDI2, SDS6, YNL330C, N0305 / Production host: ![]() #9: Protein | Mass: 45266.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: EAF3 / Production host: ![]() #10: Protein | Mass: 78951.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: RCO1 / Production host: ![]() |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 108340.836 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#6: DNA chain | Mass: 109079.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 1 types, 7 molecules ![](data/chem/img/ZN.gif)
#11: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Rpd3S histone deacetylase in complex with nucleosome / Type: COMPLEX / Entity ID: #1-#10 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.80 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.5 Details: 20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: 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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 44 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81856 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |