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- EMDB-41182: Cryo-EM map of the Unmodified nucleosome core particle in 100 mM ... -

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Basic information

Entry
Database: EMDB / ID: EMD-41182
TitleCryo-EM map of the Unmodified nucleosome core particle in 100 mM KCl with local resolution values
Map dataUnsharpened map of unmodified nucleosome core particle, 100 mM KCl
Sample
  • Complex: Nucleosome core particle
KeywordsNucleosome core particle / local resolution / PARylation / PARP / NUCLEAR PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHuang SK / Kay LE / Rubinstein JL
Funding support Canada, 4 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FND-50357 Canada
Canadian Institutes of Health Research (CIHR)FND-148375 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)2015-04347 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)2016-06718 Canada
CitationJournal: Mol Cell / Year: 2024
Title: Poly(ADP-ribosyl)ation enhances nucleosome dynamics and organizes DNA damage repair components within biomolecular condensates.
Authors: Michael L Nosella / Tae Hun Kim / Shuya Kate Huang / Robert W Harkness / Monica Goncalves / Alisia Pan / Maria Tereshchenko / Siavash Vahidi / John L Rubinstein / Hyun O Lee / Julie D Forman-Kay / Lewis E Kay /
Abstract: Nucleosomes, the basic structural units of chromatin, hinder recruitment and activity of various DNA repair proteins, necessitating modifications that enhance DNA accessibility. Poly(ADP-ribosyl) ...Nucleosomes, the basic structural units of chromatin, hinder recruitment and activity of various DNA repair proteins, necessitating modifications that enhance DNA accessibility. Poly(ADP-ribosyl)ation (PARylation) of proteins near damage sites is an essential initiation step in several DNA-repair pathways; however, its effects on nucleosome structural dynamics and organization are unclear. Using NMR, cryoelectron microscopy (cryo-EM), and biochemical assays, we show that PARylation enhances motions of the histone H3 tail and DNA, leaving the configuration of the core intact while also stimulating nuclease digestion and ligation of nicked nucleosomal DNA by LIG3. PARylation disrupted interactions between nucleosomes, preventing self-association. Addition of LIG3 and XRCC1 to PARylated nucleosomes generated condensates that selectively partition DNA repair-associated proteins in a PAR- and phosphorylation-dependent manner in vitro. Our results establish that PARylation influences nucleosomes across different length scales, extending from the atom-level motions of histone tails to the mesoscale formation of condensates with selective compositions.
History
DepositionJul 6, 2023-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41182.png

Downloads & links

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Map

FileDownload / File: emd_41182.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map of unmodified nucleosome core particle, 100 mM KCl
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 256 pix.
= 263.68 Å		1.03 Å/pix.
x 256 pix.
= 263.68 Å		1.03 Å/pix.
x 256 pix.
= 263.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-0.7985666 - 1.811855
Average (Standard dev.)0.0018519853 (±0.0716323)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 263.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map of unmodified nucleosome core particle, 100 mM KCl

Fileemd_41182_additional_1.map
AnnotationSharpened map of unmodified nucleosome core particle, 100 mM KCl
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local resolution map for the map of unmodified...

Fileemd_41182_additional_2.map
AnnotationLocal resolution map for the map of unmodified nucleosome core particle, 100 mM KCl
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map (A) of unmodified nucleosome core particle, 100 mM KCl

Fileemd_41182_half_map_1.map
AnnotationHalf map (A) of unmodified nucleosome core particle, 100 mM KCl
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map (B) of unmodified nucleosome core particle, 100 mM KCl

Fileemd_41182_half_map_2.map
AnnotationHalf map (B) of unmodified nucleosome core particle, 100 mM KCl
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Nucleosome core particle

EntireName: Nucleosome core particle
Components
  • Complex: Nucleosome core particle

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Supramolecule #1: Nucleosome core particle

SupramoleculeName: Nucleosome core particle / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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