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- EMDB-53927: Cryo-ET of endothelial cells cultured on electrospun gelatin fibers -

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Basic information

Entry
Database: EMDB / ID: EMD-53927
TitleCryo-ET of endothelial cells cultured on electrospun gelatin fibers
Map dataCryo-ET of HUVEC endothelial cells cultured on electrospun gelatin fibers
Sample
  • Cell: HUVEC Cells
KeywordsCell / ECM model / CELL ADHESION
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsTcherner Elad S / Vilensky R / Ben-Asher N / Logvina N / Zalk R / Zussman E / Engel L
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation1925/23 Israel
CitationJournal: Nanoscale / Year: 2025
Title: An engineered platform to study the influence of extracellular matrix nanotopography on cell ultrastructure.
Authors: Shani Tcherner Elad / Rita Vilensky / Noa Ben Asher / Nataliya Logvina / Ran Zalk / Eyal Zussman / Leeya Engel /
Abstract: Nanoscale fabrication techniques have played an essential role in revealing the impact of extracellular matrix (ECM) nanotopography on cellular behavior. However, the mechanisms by which ...Nanoscale fabrication techniques have played an essential role in revealing the impact of extracellular matrix (ECM) nanotopography on cellular behavior. However, the mechanisms by which nanotopographical cues from the ECM influence cellular function remain unclear. To approach these questions, we have engineered a novel class of nanopatterned ECM constructs suitable for cryogenic electron tomography (cryo-ET), the highest resolution modality for imaging frozen hydrated cells in 3D. We electrospun aligned and randomly oriented ECM fibers directly onto transmission electron microscopy (TEM) supports to generate fibrous scaffolds that mimic physiological ECM in healthy (organized ECM) and diseased (disorganized ECM) states. We produced fibers from gelatin without toxic additives and cross-linked them to maintain structural stability in aqueous environments. The electrospun fibers had an average fiber diameter of hundreds of nanometers. We confirmed that the nanopatterned TEM supports can serve as viable cell culture substrates that can influence cell organization and demonstrated their compatibility with plunge freezing and cryo-ET. By enabling nanoscale structural analysis inside cells on substrates with programmable topographies, this platform can be used to study the physical cues necessary for healthy endothelial tissue formation and pathologies that are linked to endothelial dysfunction in diseases such as peripheral arterial disease.
History
DepositionJun 1, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53927.png

Downloads & links

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Map

FileDownload / File: emd_53927.map.gz / Format: CCP4 / Size: 106 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationCryo-ET of HUVEC endothelial cells cultured on electrospun gelatin fibers
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
12.25 Å/pix.
x 106 pix.
= 1298.5 Å		12.25 Å/pix.
x 1024 pix.
= 12544. Å		12.25 Å/pix.
x 1024 pix.
= 12544. 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: 12.25 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)1.0817982 (±31.150711000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-51
Dimensions10241024106
Spacing10241024106
CellA: 12544.0 Å / B: 12544.0 Å / C: 1298.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Cryo-ET of HUVEC endothelial cells cultured on electrospun...

Fileemd_53927_additional_1.map
AnnotationCryo-ET of HUVEC endothelial cells cultured on electrospun gelatin fibers
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Cryo-ET of HUVEC endothelial cells cultured on electrospun...

Fileemd_53927_additional_2.map
AnnotationCryo-ET of HUVEC endothelial cells cultured on electrospun gelatin fibers
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HUVEC Cells

EntireName: HUVEC Cells
Components
  • Cell: HUVEC Cells

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Supramolecule #1: HUVEC Cells

SupramoleculeName: HUVEC Cells / type: cell / ID: 1 / Parent: 0
Details: Example tomograms of endothelial cells cultured on electrospun gelatin fibers
Source (natural)Organism: Homo sapiens (human) / Strain: HUVECs, Sciencell 8000-SCL

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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 / Details: PBS
GridModel: Quantifoil / Material: GOLD / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP / Details: Leica EM GP2.
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris X
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 9.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 39000

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 41
CTF correctionSoftware - Name: IMOD (ver. 5.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

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