+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41449 | ||||||||||||||||||
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Title | Rpd3S bound to an H3K36Cme3 modified nucleosome | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Keywords | nucleosome / methylation / acetylation / Rpd3S / TRANSCRIPTION / TRANSCRIPTION-DNA complex | ||||||||||||||||||
Function / homology | Function and homology information 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 / negative regulation of rDNA heterochromatin formation / Rpd3L complex / 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 / negative regulation of rDNA heterochromatin formation / Rpd3L complex / Rpd3S complex / Rpd3L-Expanded complex / rDNA chromatin condensation / regulation of RNA stability / nucleophagy / HDACs deacetylate histones / DNA replication-dependent chromatin assembly / nucleosome disassembly / NuRD complex / histone deacetylase / 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 / Estrogen-dependent gene expression / histone deacetylase complex / positive regulation of macroautophagy / histone acetyltransferase complex / nuclear periphery / 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 / nucleosome / nucleosome assembly / response to oxidative stress / transcription coactivator activity / cell cycle / 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 | Saccharomyces cerevisiae (brewer's yeast) / Xenopus laevis (African clawed frog) / synthetic construct (others) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||||||||||||||
Authors | Markert JW / Vos SM / Farnung L | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: Nat Commun / Year: 2023 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
Supplemental images |
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-Downloads & links
-EMDB archive
-Validation report
Summary document | emd_41449_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_41449_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_41449_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | emd_41449_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41449 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41449 | HTTPS FTP |
-Related structure data
Related structure data | 8tofMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41449.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.822 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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-Sample components
+Entire : Rpd3S bound to H3K36Cme3 nucleosome
+Supramolecule #1: Rpd3S bound to H3K36Cme3 nucleosome
+Macromolecule #1: Transcriptional regulatory protein SIN3
+Macromolecule #2: Histone deacetylase RPD3
+Macromolecule #3: Chromatin modification-related protein EAF3
+Macromolecule #4: Transcriptional regulatory protein RCO1
+Macromolecule #5: Rco1
+Macromolecule #8: Histone H3
+Macromolecule #9: Histone H4
+Macromolecule #10: Histone H2A
+Macromolecule #11: Histone H2B 1.1
+Macromolecule #12: histone N-terminal tail
+Macromolecule #6: DNA (176-MER)
+Macromolecule #7: DNA (176-MER)
+Macromolecule #13: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 484141 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: ANGULAR RECONSTITUTION |