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- EMDB-41147: H1-nucleosome (chromatosome) -

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Basic information

Entry
Database: EMDB / ID: EMD-41147
TitleH1-nucleosome (chromatosome)
Map dataH1-nucleosome (chromatosome), 3DFlex reconstruction, locally filtered
Sample
  • Complex: H1-nucleosome (chromatosome)
Keywordsnucleosome / gene repression / epigenetics / chromatin / GENE REGULATION
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSauer PV / Pavlenko E / Nogales E / Poepsel S
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: 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
DepositionJun 28, 2023-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41147.png

Downloads & links

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Map

FileDownload / File: emd_41147.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationH1-nucleosome (chromatosome), 3DFlex reconstruction, locally filtered
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 384 pix.
= 437.76 Å		1.14 Å/pix.
x 384 pix.
= 437.76 Å		1.14 Å/pix.
x 384 pix.
= 437.76 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.027410753 - 0.07288345
Average (Standard dev.)0.00008810775 (±0.0014111163)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 437.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41147_msk_1.map
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Additional map: H1-nucleosome (chromatosome), non-uniform refinement

Fileemd_41147_additional_1.map
AnnotationH1-nucleosome (chromatosome), non-uniform refinement
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Additional map: H1-nucleosome (chromatosome), 3DFlex reconstruction, half map A

Fileemd_41147_additional_2.map
AnnotationH1-nucleosome (chromatosome), 3DFlex reconstruction, half map A
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Additional map: H1-nucleosome (chromatosome), 3DFlex reconstruction, half map B

Fileemd_41147_additional_3.map
AnnotationH1-nucleosome (chromatosome), 3DFlex reconstruction, half map B
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Half map: H1-nucleosome (chromatosome), non-uniform refinement, map half A

Fileemd_41147_half_map_1.map
AnnotationH1-nucleosome (chromatosome), non-uniform refinement, map half A
Projections & Slices
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Half map: H1-nucleosome (chromatosome), non-uniform refinement, map half B

Fileemd_41147_half_map_2.map
AnnotationH1-nucleosome (chromatosome), non-uniform refinement, map half B
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : H1-nucleosome (chromatosome)

EntireName: H1-nucleosome (chromatosome)
Components
  • Complex: H1-nucleosome (chromatosome)

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Supramolecule #1: H1-nucleosome (chromatosome)

SupramoleculeName: H1-nucleosome (chromatosome) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 290 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
GridMaterial: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

7334

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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