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- EMDB-35060: Clr4-H3K9 Nucleosome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-35060
TitleClr4-H3K9 Nucleosome complex
Map data
Sample
  • Complex: Clr4-H3K9 Nucleosome complex
KeywordsH3K9 nucleosome / methyltransferases / Clr4 / PROTEIN BINDING
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsAkoury E
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Rep / Year: 2024
Title: Structural insights into the binding mechanism of Clr4 methyltransferase to H3K9 methylated nucleosome.
Authors: Christopher Saab / Joseph Stephan / Elias Akoury /
Abstract: The establishment and maintenance of heterochromatin, a specific chromatin structure essential for genomic stability and regulation, rely on intricate interactions between chromatin-modifying enzymes ...The establishment and maintenance of heterochromatin, a specific chromatin structure essential for genomic stability and regulation, rely on intricate interactions between chromatin-modifying enzymes and nucleosomal histone proteins. However, the precise trigger for these modifications remains unclear, thus highlighting the need for a deeper understanding of how methyltransferases facilitate histone methylation among others. Here, we investigate the molecular mechanisms underlying heterochromatin assembly by studying the interaction between the H3K9 methyltransferase Clr4 and H3K9-methylated nucleosomes. Using a combination of liquid-state nuclear magnetic resonance spectroscopy and cryo-electron microscopy, we elucidate the structural basis of Clr4 binding to H3K9-methylated nucleosomes. Our results reveal that Clr4 engages with nucleosomes through its chromodomain and disordered regions to promote de novo methylation. This study provides crucial insights into the molecular mechanisms governing heterochromatin formation by highlighting the significance of chromatin-modifying enzymes in genome regulation and disease pathology.
History
DepositionDec 31, 2022-
Header (metadata) releaseMar 22, 2023-
Map releaseMar 22, 2023-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35060.png

Downloads & links

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Map

FileDownload / File: emd_35060.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.011427009 - 0.026061784
Average (Standard dev.)0.00018111605 (±0.0014425942)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 80.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_35060_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_35060_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Clr4-H3K9 Nucleosome complex

EntireName: Clr4-H3K9 Nucleosome complex
Components
  • Complex: Clr4-H3K9 Nucleosome complex

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Supramolecule #1: Clr4-H3K9 Nucleosome complex

SupramoleculeName: Clr4-H3K9 Nucleosome complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 230 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: 6.8
GridMaterial: COPPER
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Average electron dose: 15.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: COMMON LINE
Final reconstructionAlgorithm: ALGEBRAIC (ARTS) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 1200000

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