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Open data
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Basic information
Entry | Database: PDB / ID: 8tof | ||||||||||||||||||
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Title | Rpd3S bound to an H3K36Cme3 modified nucleosome | ||||||||||||||||||
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![]() | TRANSCRIPTION/DNA / nucleosome / methylation / acetylation / Rpd3S / TRANSCRIPTION / TRANSCRIPTION-DNA complex | ||||||||||||||||||
Function / homology | ![]() nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / protein localization to nucleolar rDNA repeats / Rpd3L complex / negative regulation of rDNA heterochromatin formation / Rpd3S complex / Rpd3L-Expanded complex ...nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / protein localization to nucleolar rDNA repeats / Rpd3L complex / negative regulation of rDNA heterochromatin formation / Rpd3S complex / Rpd3L-Expanded complex / rDNA chromatin condensation / regulation of RNA stability / nucleophagy / HDACs deacetylate histones / DNA replication-dependent chromatin assembly / NuRD complex / histone deacetylase / SUMOylation of chromatin organization proteins / nucleosome disassembly / 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 / histone acetyltransferase complex / nuclear periphery / meiotic cell cycle / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / double-strand break repair via nonhomologous end joining / 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 / protein heterodimerization activity / cell division / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription / 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: 2.8 Å | ||||||||||||||||||
![]() | Markert, J.W. / Vos, S.M. / Farnung, L. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the complete Saccharomyces cerevisiae Rpd3S-nucleosome complex. Authors: Jonathan W Markert / Seychelle M Vos / Lucas Farnung / ![]() Abstract: Acetylation of histones is a key post-translational modification that guides gene expression regulation. In yeast, the class I histone deacetylase containing Rpd3S complex plays a critical role in ...Acetylation of histones is a key post-translational modification that guides gene expression regulation. In yeast, the class I histone deacetylase containing Rpd3S complex plays a critical role in the suppression of spurious transcription by removing histone acetylation from actively transcribed genes. The S. cerevisiae Rpd3S complex has five subunits (Rpd3, Sin3, Rco1, Eaf3, and Ume1) but its subunit stoichiometry and how the complex engages nucleosomes to achieve substrate specificity remains elusive. Here we report the cryo-EM structure of the complete Rpd3S complex bound to a nucleosome. Sin3 and two copies of subunits Rco1 and Eaf3 encircle the deacetylase subunit Rpd3 and coordinate the positioning of Ume1. The Rpd3S complex binds both trimethylated H3 tails at position lysine 36 and makes multiple additional contacts with the nucleosomal DNA and the H2A-H2B acidic patch. Direct regulation via the Sin3 subunit coordinates binding of the acetylated histone substrate to achieve substrate specificity. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 774.5 KB | Display | ![]() |
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PDB format | ![]() | 586 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 41449MC 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
-Transcriptional regulatory protein ... , 2 types, 3 molecules AFG
#1: 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: ![]() |
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#4: Protein | Mass: 78951.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: RCO1 / Production host: ![]() |
-Protein , 6 types, 11 molecules BDEaebfcgdh
#2: 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: ![]() | ||||||||
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#3: Protein | Mass: 45266.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: EAF3 / Production host: ![]() #8: Protein | Mass: 15495.247 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #9: Protein | Mass: 11394.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #10: Protein | Mass: 14109.436 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #11: Protein | Mass: 13655.948 Da / Num. of mol.: 2 / Mutation: S29T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein/peptide , 2 types, 2 molecules Hx
#5: Protein/peptide | Mass: 515.628 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() |
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#12: Protein/peptide | Mass: 657.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-DNA chain , 2 types, 2 molecules NT
#6: DNA chain | Mass: 63931.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#7: DNA chain | Mass: 66097.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 1 types, 5 molecules ![](data/chem/img/ZN.gif)
#13: 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 bound to H3K36Cme3 nucleosome / Type: COMPLEX / Entity ID: #1-#12 / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: 2250 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 51.1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 484141 / Symmetry type: POINT |