+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41147 | |||||||||
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Title | H1-nucleosome (chromatosome) | |||||||||
Map data | H1-nucleosome (chromatosome), 3DFlex reconstruction, locally filtered | |||||||||
Sample |
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Keywords | nucleosome / gene repression / epigenetics / chromatin / GENE REGULATION | |||||||||
Biological species | Xenopus laevis (African clawed frog) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Sauer PV / Pavlenko E / Nogales E / Poepsel S | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Mol Cell / Year: 2024 Title: Activation of automethylated PRC2 by dimerization on chromatin. Authors: Paul V Sauer / Egor Pavlenko / Trinity Cookis / Linda C Zirden / Juliane Renn / Ankush Singhal / Pascal Hunold / Michaela N Hoehne-Wiechmann / Olivia van Ray / Farnusch Kaschani / Markus ...Authors: Paul V Sauer / Egor Pavlenko / Trinity Cookis / Linda C Zirden / Juliane Renn / Ankush Singhal / Pascal Hunold / Michaela N Hoehne-Wiechmann / Olivia van Ray / Farnusch Kaschani / Markus Kaiser / Robert Hänsel-Hertsch / Karissa Y Sanbonmatsu / Eva Nogales / Simon Poepsel / Abstract: Polycomb repressive complex 2 (PRC2) is an epigenetic regulator that trimethylates lysine 27 of histone 3 (H3K27me3) and is essential for embryonic development and cellular differentiation. H3K27me3 ...Polycomb repressive complex 2 (PRC2) is an epigenetic regulator that trimethylates lysine 27 of histone 3 (H3K27me3) and is essential for embryonic development and cellular differentiation. H3K27me3 is associated with transcriptionally repressed chromatin and is established when PRC2 is allosterically activated upon methyl-lysine binding by the regulatory subunit EED. Automethylation of the catalytic subunit enhancer of zeste homolog 2 (EZH2) stimulates its activity by an unknown mechanism. Here, we show that human PRC2 forms a dimer on chromatin in which an inactive, automethylated PRC2 protomer is the allosteric activator of a second PRC2 that is poised to methylate H3 of a substrate nucleosome. Functional assays support our model of allosteric trans-autoactivation via EED, suggesting a previously unknown mechanism mediating context-dependent activation of PRC2. Our work showcases the molecular mechanism of auto-modification-coupled dimerization in the regulation of chromatin-modifying complexes. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41147.map.gz | 201.7 MB | EMDB map data format | |
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Header (meta data) | emd-41147-v30.xml emd-41147.xml | 21.4 KB 21.4 KB | Display Display | EMDB header |
Images | emd_41147.png | 43 KB | ||
Masks | emd_41147_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-41147.cif.gz | 4.4 KB | ||
Others | emd_41147_additional_1.map.gz emd_41147_additional_2.map.gz emd_41147_additional_3.map.gz emd_41147_half_map_1.map.gz emd_41147_half_map_2.map.gz | 109.1 MB 3 MB 3 MB 200.4 MB 200.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41147 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41147 | HTTPS FTP |
-Validation report
Summary document | emd_41147_validation.pdf.gz | 736.7 KB | Display | EMDB validaton report |
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Full document | emd_41147_full_validation.pdf.gz | 736.3 KB | Display | |
Data in XML | emd_41147_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | emd_41147_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41147 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41147 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41147.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | H1-nucleosome (chromatosome), 3DFlex reconstruction, locally filtered | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.14 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41147_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: H1-nucleosome (chromatosome), non-uniform refinement
File | emd_41147_additional_1.map | ||||||||||||
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Annotation | H1-nucleosome (chromatosome), non-uniform refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: H1-nucleosome (chromatosome), 3DFlex reconstruction, half map A
File | emd_41147_additional_2.map | ||||||||||||
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Annotation | H1-nucleosome (chromatosome), 3DFlex reconstruction, half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: H1-nucleosome (chromatosome), 3DFlex reconstruction, half map B
File | emd_41147_additional_3.map | ||||||||||||
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Annotation | H1-nucleosome (chromatosome), 3DFlex reconstruction, half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: H1-nucleosome (chromatosome), non-uniform refinement, map half A
File | emd_41147_half_map_1.map | ||||||||||||
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Annotation | H1-nucleosome (chromatosome), non-uniform refinement, map half A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: H1-nucleosome (chromatosome), non-uniform refinement, map half B
File | emd_41147_half_map_2.map | ||||||||||||
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Annotation | H1-nucleosome (chromatosome), non-uniform refinement, map half B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : H1-nucleosome (chromatosome)
Entire | Name: H1-nucleosome (chromatosome) |
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Components |
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-Supramolecule #1: H1-nucleosome (chromatosome)
Supramolecule | Name: H1-nucleosome (chromatosome) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13 |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 290 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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Grid | Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY |
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) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 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: 2.5 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44000 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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