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- EMDB-58008: 2.3 angstrom cryoEM map of endogenous nucleosome core particle in... -

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Basic information

Entry
Database: EMDB / ID: EMD-58008
Title2.3 angstrom cryoEM map of endogenous nucleosome core particle in nuclear lysate
Map data
Sample
  • Complex: Endogenous nucleosome core particle
KeywordsNucleosome / Genome / Nucleoprotein / NUCLEAR PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsKer DS / Pellegrini L
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Citation
Journal: Biosci Rep / Year: 2026
Title: High-resolution cryoEM of nucleosomes in nuclear extracts of mammalian cells.
Authors: De-Sheng Ker / Hedaya Aboalnaga / Luca Pellegrini /
Abstract: Frontier Structural Biology methods are transitioning from analysis of reconstituted macromolecular complexes in vitro to imaging of macromolecular assemblies within the physiological confines of the ...Frontier Structural Biology methods are transitioning from analysis of reconstituted macromolecular complexes in vitro to imaging of macromolecular assemblies within the physiological confines of the cell. Preparation of samples for in situ cryoEM analysis requires FIB milling or ultramicrotome sectioning, laborious and technically challenging procedures that are low-throughput and require a high degree of technical skills. We have devised a simple approach for cryoEM of nuclear macromolecular complexes that preserves to a high degree their physiological environment while removing the need for thin sectioning of the sample. The method requires only the preparation of nuclear extracts without additional purification or enrichment steps. We applied the method to obtain a 2.3 Å cryoEM structure of nucleosomes visualised directly in the nuclear lysate of human cells.
#1: Journal: Biorxiv / Year: 2026
Title: High-resolution cryoEM of nucleosomes in nuclear extracts of mammalian cells
Authors: Ker DS / Aboalnaga H / Pellegrini L
History
DepositionMay 12, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58008.png

Downloads & links

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Map

FileDownload / File: emd_58008.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 416 pix.
= 386.464 Å		0.93 Å/pix.
x 416 pix.
= 386.464 Å		0.93 Å/pix.
x 416 pix.
= 386.464 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.929 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0516
Minimum - Maximum-0.12124127 - 0.41646373
Average (Standard dev.)0.000019891359 (±0.0050893957)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 386.46402 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_58008_msk_1.map
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Additional map: Post-processed map by DeepEMhancer software

Fileemd_58008_additional_1.map
AnnotationPost-processed map by DeepEMhancer software
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Half map: #2

Fileemd_58008_half_map_1.map
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Half map: #1

Fileemd_58008_half_map_2.map
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Sample components

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Entire : Endogenous nucleosome core particle

EntireName: Endogenous nucleosome core particle
Components
  • Complex: Endogenous nucleosome core particle

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Supramolecule #1: Endogenous nucleosome core particle

SupramoleculeName: Endogenous nucleosome core particle / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average exposure time: 4.39 sec. / Average electron dose: 47.36 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: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 286667
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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