+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33849 | |||||||||||||||
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Title | Cryo-EM map of Rpd3S in loose-state Rpd3S-NCP complex | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | Dynamic Histone Modifications / Gene Regulation / Histone Deacetylase 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 / Rpd3S complex / Rpd3L 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 / Rpd3S complex / Rpd3L 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 / transcription corepressor activity / nucleosome assembly / response to oxidative stress / transcription coactivator activity / cell cycle / 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 / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | synthetic construct (others) / Saccharomyces cerevisiae S288C (yeast) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||||||||
Authors | Li HT / Yan CY / Guan HP / Wang P | |||||||||||||||
Funding support | China, 4 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33849.map.gz | 7.1 MB | EMDB map data format | |
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Header (meta data) | emd-33849-v30.xml emd-33849.xml | 25.5 KB 25.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33849_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_33849.png | 141.3 KB | ||
Others | emd_33849_half_map_1.map.gz emd_33849_half_map_2.map.gz | 80.8 MB 80.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33849 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33849 | HTTPS FTP |
-Validation report
Summary document | emd_33849_validation.pdf.gz | 736.3 KB | Display | EMDB validaton report |
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Full document | emd_33849_full_validation.pdf.gz | 735.9 KB | Display | |
Data in XML | emd_33849_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | emd_33849_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33849 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33849 | HTTPS FTP |
-Related structure data
Related structure data | 7yi2MC 7yi0C 7yi1C 7yi3C 7yi4C 7yi5C C: citing same article (ref.) M: atomic model generated by this map |
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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_33849.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.0825 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_33849_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33849_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Rpd3S complex with H3K36me3 nucleosome
+Supramolecule #1: Rpd3S complex with H3K36me3 nucleosome
+Supramolecule #2: DNA
+Supramolecule #3: SIN3/RPD3/EAF3/RCO1
+Macromolecule #1: Wisdom 601 DNA (167-MER)
+Macromolecule #2: Wisdom 601 DNA (167-MER)
+Macromolecule #3: Transcriptional regulatory protein SIN3
+Macromolecule #4: Histone deacetylase RPD3
+Macromolecule #5: Chromatin modification-related protein EAF3
+Macromolecule #6: Transcriptional regulatory protein RCO1
+Macromolecule #7: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.7 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 1.8 µm / Calibrated defocus min: 1.5 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |