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- EMDB-55310: CryoCARE-denoised tomogram of two cholesterol-depleted HEK293 cel... -

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Basic information

Entry
Database: EMDB / ID: EMD-55310
TitleCryoCARE-denoised tomogram of two cholesterol-depleted HEK293 cells in close contact
Map dataCryoCARE-denoised tomogram (bin4) containing two HEK293 cells treated for 30 min with 10 mM MBCD in close contact. Visible features include both plasma membranes and the mitochondria of one cell.
Sample
  • Cell: CryoCARE-denoised tomogram of two cholesterol-depleted HEK293 cells in close contact
Keywordsplasma membrane / UNKNOWN FUNCTION
Biological speciesHEK293 (human)
Methodelectron tomography / cryo EM
AuthorsGlushkova D / Boehm S / Beck M
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: J Cell Biol / Year: 2026
Title: Systematic membrane thickness variation across cellular organelles revealed by cryo-ET.
Authors: Desislava Glushkova / Stefanie Böhm / Martin Beck /
Abstract: In eukaryotes, membrane-bound organelles create distinct molecular environments. The compartmentalizing lipid bilayer is a dynamic composite material whose thickness and curvature modulate the ...In eukaryotes, membrane-bound organelles create distinct molecular environments. The compartmentalizing lipid bilayer is a dynamic composite material whose thickness and curvature modulate the structure and function of membrane proteins. In vitro, bilayer thickness correlates with lipid composition. Cellular membranes in situ, however, are continuously remodeled, and the spatial variation of their biophysical properties remains understudied. Here, we present a computational approach to measure local membrane thickness in cryo-electron tomograms. Our analysis of Chlamydomonas reinhardtii and human cells reveals systematic thickness variations within and across organelles. Notably, we observe thickness gradients across the Golgi apparatus that orthogonally support long-standing models of differential sorting of transmembrane proteins based on hydrophobic matching. Our publicly available workflow readily integrates within existing tomogram analysis pipelines and, when applied across experimental systems, provides a quantitative foundation for exploring relationships between membrane thickness and function in native cellular environments.
History
DepositionOct 7, 2025-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55310.png

Downloads & links

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Map

FileDownload / File: emd_55310.map.gz / Format: CCP4 / Size: 2.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoCARE-denoised tomogram (bin4) containing two HEK293 cells treated for 30 min with 10 mM MBCD in close contact. Visible features include both plasma membranes and the mitochondria of one cell.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.88 Å/pix.
x 550 pix.
= 4336.2 Å		7.88 Å/pix.
x 1024 pix.
= 8073.216 Å		7.88 Å/pix.
x 1024 pix.
= 8073.216 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 7.884 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-0.033107884 - 0.01337651
Average (Standard dev.)-0.000013614696 (±0.0006266287)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions10241024550
Spacing10241024550
CellA: 8073.216 Å / B: 8073.216 Å / C: 4336.1997 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : CryoCARE-denoised tomogram of two cholesterol-depleted HEK293 cel...

EntireName: CryoCARE-denoised tomogram of two cholesterol-depleted HEK293 cells in close contact
Components
  • Cell: CryoCARE-denoised tomogram of two cholesterol-depleted HEK293 cells in close contact

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Supramolecule #1: CryoCARE-denoised tomogram of two cholesterol-depleted HEK293 cel...

SupramoleculeName: CryoCARE-denoised tomogram of two cholesterol-depleted HEK293 cells in close contact
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: HEK293 (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4 / Component - Concentration: 10.0 mM / Component - Name: Methyl-beta-cyclodextrin
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: SILICON DIOXIDE / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.1 / Focused ion beam - Duration: 3600 / Focused ion beam - Temperature: 80 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Aquilos 2 FIB-SEM. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 61
CTF correctionType: NONE

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