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- EMDB-15481: Subtomogram average of nucleosomes extracted from euchromatin and... -

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Basic information

Entry
Database: EMDB / ID: EMD-15481
TitleSubtomogram average of nucleosomes extracted from euchromatin and facultative heterochromatin nanodomains of Drosophila melanogaster embryos
Map data
Sample
  • Complex: nucleosome
Keywordsnucleosome tomography chromatin / STRUCTURAL GENOMICS
Biological speciesDrosophila melanogaster (fruit fly)
Methodsubtomogram averaging / cryo EM / Resolution: 13.5 Å
AuthorsFatmaoui F / Eltsov M / Leforestier A
Funding support France, Germany, 4 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE11-0020-01 France
Agence Nationale de la Recherche (ANR)ANR-20-CE11-0020-03 France
Agence Nationale de la Recherche (ANR)ANR-19-CE11-0008-01 France
German Research Foundation (DFG)EL 861/1 Germany
CitationJournal: To Be Published
Title: Cryo-electron tomography and deep learning-based denoising reveal native chromatin landscapes of interphase nuclei
Authors: Fatmaoui F / Carrivain P / Grewe D / Jakob B / Victor JM / Leforestier A / Eltsov M
History
DepositionJul 28, 2022-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateAug 16, 2023-
Current statusAug 16, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15481.png

Downloads & links

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Map

FileDownload / File: emd_15481.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.25 Å/pix.
x 64 pix.
= 272. Å		4.25 Å/pix.
x 64 pix.
= 272. Å		4.25 Å/pix.
x 64 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.218
Minimum - Maximum-0.26920947 - 0.6983119
Average (Standard dev.)0.0056329565 (±0.055572942)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-32-32-32
Dimensions646464
Spacing646464
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_15481_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15481_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 : nucleosome

EntireName: nucleosome
Components
  • Complex: nucleosome

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Supramolecule #1: nucleosome

SupramoleculeName: nucleosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 210 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.5
GridModel: C-flat-2/2 / Material: COPPER/PALLADIUM / Mesh: 200 / Support film - Material: CARBON
VitrificationCryogen name: OTHER / Details: high pressure freezer HPM010 (ABRA Fluid AG).
DetailsDrosophila melanogaster embryos were high-pressure frozen. Vitreous sections were cut with a nominal thickness of 75 nm and collected onto 200 mesh C-flat grids

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.25 µm / Nominal defocus min: 0.25 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 13.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 549
ExtractionNumber tomograms: 1 / Number images used: 552
Final angle assignmentType: NOT APPLICABLE

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