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- EMDB-54985: Subtomogram average of nucleosomes extracted from vitreous sectio... -

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Basic information

Entry
Database: EMDB / ID: EMD-54985
TitleSubtomogram average of nucleosomes extracted from vitreous sections of Drosophila melanogaster embryos
Map datamap
Sample
  • Complex: nucleosome
Keywordsnucleosome / DNA BINDING PROTEIN
Biological speciesDrosophila melanogaster (fruit fly)
Methodsubtomogram averaging / cryo EM / Resolution: 20.0 Å
AuthorsFatmaoui F / Iusupova A / Grewe D / Taiki F / Leforestier A / Eltsov M
Funding support France, Germany, 5 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE11-0020-01 France
Agence Nationale de la Recherche (ANR)ANR-20-CE11-0020-02 France
Agence Nationale de la Recherche (ANR)ANR-20-CE11-0020-04 France
German Research Foundation (DFG)EL 861/1 Germany
Agence Nationale de la Recherche (ANR)ANR-10-INSB-005 France
CitationJournal: EMBO J / Year: 2026
Title: Direct visualization and tracing of chromatin folding in the Drosophila embryo.
Authors: Fadwa Fatmaoui / Pascal Carrivain / Fatima Taiki / Amina Iusupova / Diana Grewe / Wim Hagen / Burkhard Jakob / Jean-Marc Victor / Amélie Leforestier / Mikhail Eltsov /
Abstract: Chromatin organization, through the assembly of DNA with histones and the folding of nucleosome chains, regulates DNA accessibility for transcription, DNA replication and repair. Although models ...Chromatin organization, through the assembly of DNA with histones and the folding of nucleosome chains, regulates DNA accessibility for transcription, DNA replication and repair. Although models derived from in vitro studies have proposed distinct nucleosome chain geometries, the organization of chromatin within the crowded cell nucleus remains elusive. Using cryo-electron tomography of thin vitreous sections, we directly observed the path of nucleosomal and linker DNA in situ from a flash-frozen organism - Drosophila embryos. We quantified linker length and curvature, characterizing an irregular zig-zag chromatin-folding motif, with a low degree of linker bending. Nucleosome conformations could be identified on individual particles in favorable orientations without structure averaging. Additionally, we observed particles that accommodate a number of DNA gyres ranging from less than one to up to three, which resemble previously proposed non-octameric nucleosomal particles with variable DNA wrapping.
History
DepositionSep 3, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54985.png

Downloads & links

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Map

FileDownload / File: emd_54985.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 4.25 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-0.21531253 - 0.66935664
Average (Standard dev.)-0.0005372114 (±0.057328008)
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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Mask #1

Fileemd_54985_msk_1.map
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AxesZYX

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Half map: odd half map

Fileemd_54985_half_map_1.map
Annotationodd half map
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Histogram (log scale)

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Half map: even half map

Fileemd_54985_half_map_2.map
Annotationeven half map
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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: 200 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
VitrificationCryogen name: NITROGEN / Details: high pressure freezer HPM010.
DetailsDrosophila embryo

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 3.0 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: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: AV3 / Number subtomograms used: 2000
ExtractionNumber tomograms: 3 / Number images used: 2000 / Software - Name: IMOD
CTF correctionType: NONE
Final angle assignmentType: OTHER

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