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- EMDB-51962: Thin edge of an U2OS cell. -

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Basic information

Entry
Database: EMDB / ID: EMD-51962
TitleThin edge of an U2OS cell.
Map dataTomogram of a thin edge of an U2OS cell.
Sample
  • Cell: U2OS cell grown on a Quantifoil grid.
Keywordscytoplasm / filaments / vesicles / CYTOSOLIC PROTEIN
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsSzwedziak P
Funding support Poland, 1 items
OrganizationGrant numberCountry
Foundation for Polish ScienceMAB/20172 Poland
CitationJournal: Biorxiv / Year: 2024
Title: In situ structural analysis of mammalian cells using a 200 kV electron cryomicroscope: implications for research infrastructure.
Authors: Szwedziak P
History
DepositionOct 30, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51962.png

Downloads & links

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Map

FileDownload / File: emd_51962.map.gz / Format: CCP4 / Size: 502.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomogram of a thin edge of an U2OS cell.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
20.54 Å/pix.
x 135 pix.
= 2772.9 Å		20.54 Å/pix.
x 984 pix.
= 20211.361 Å		20.54 Å/pix.
x 992 pix.
= 20375.682 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: 20.54 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-1.0556221 - 7.258441
Average (Standard dev.)2.99794 (±0.34768093)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin715-247
Dimensions984992135
Spacing992984135
CellA: 20375.682 Å / B: 20211.361 Å / C: 2772.9001 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : U2OS cell grown on a Quantifoil grid.

EntireName: U2OS cell grown on a Quantifoil grid.
Components
  • Cell: U2OS cell grown on a Quantifoil grid.

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Supramolecule #1: U2OS cell grown on a Quantifoil grid.

SupramoleculeName: U2OS cell grown on a Quantifoil grid. / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (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
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 310 K / Instrument: FEI VITROBOT MARK IV
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Cytodiagnostics / Diameter: 10 nm

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 3.78 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 7.0 µm / Nominal defocus min: 5.0 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Final reconstructionNumber images used: 37

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