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- EMDB-16179: Deconvolved dual-axis CSTET tomogram of a WI-38 fibroblast cell a... -

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Basic information

Entry
Database: EMDB / ID: EMD-16179
TitleDeconvolved dual-axis CSTET tomogram of a WI-38 fibroblast cell at 850 nm thick part
Map dataDeconvolved dual-axis CSTET tomogram of a WI38 fibroblast cell
Sample
  • Cell: WI-38 fibroblast
KeywordsMitochondria-ER contact / whole cell tomography / UNKNOWN FUNCTION
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsKirchweger P / Mullick D / Elbaum M
Funding support Austria, Israel, European Union, 4 items
OrganizationGrant numberCountry
Austrian Science FundJ4449-B Austria
Israel Science Foundation1696/18 Israel
European Union (EU)IMpaCT (grant no.857203)European Union
European Research Council (ERC)101055413European Union
CitationJournal: J Struct Biol / Year: 2023
Title: Correlating cryo-super resolution radial fluctuations and dual-axis cryo-scanning transmission electron tomography to bridge the light-electron resolution gap.
Authors: Peter Kirchweger / Debakshi Mullick / Prabhu Prasad Swain / Sharon G Wolf / Michael Elbaum /
Abstract: Visualization of organelles and their interactions with other features in the native cell remains a challenge in modern biology. We have introduced cryo-scanning transmission electron tomography ...Visualization of organelles and their interactions with other features in the native cell remains a challenge in modern biology. We have introduced cryo-scanning transmission electron tomography (CSTET), which can access 3D volumes on the scale of 1 micron with a resolution of nanometers, making it ideal for this task. Here we introduce two relevant advances: (a) we demonstrate the utility of multi-color super-resolution radial fluctuation light microscopy under cryogenic conditions (cryo-SRRF), and (b) we extend the use of deconvolution processing for dual-axis CSTET data. We show that cryo-SRRF nanoscopy is able to reach resolutions in the range of 100 nm, using commonly available fluorophores and a conventional widefield microscope for cryo-correlative light-electron microscopy. Such resolution aids in precisely identifying regions of interest before tomographic acquisition and enhances precision in localizing features of interest within the 3D reconstruction. Dual-axis CSTET tilt series data and application of entropy regularized deconvolution during post-processing results in close-to-isotropic resolution in the reconstruction without averaging. The integration of cryo-SRRF with deconvolved dual-axis CSTET provides a versatile workflow for studying unique objects in a cell.
History
DepositionNov 19, 2022-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateAug 23, 2023-
Current statusAug 23, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16179.png

Downloads & links

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Map

FileDownload / File: emd_16179.map.gz / Format: CCP4 / Size: 788 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeconvolved dual-axis CSTET tomogram of a WI38 fibroblast cell
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
40.84 Å/pix.
x 197 pix.
= 8045.48 Å		40.84 Å/pix.
x 1024 pix.
= 41820.16 Å		40.84 Å/pix.
x 1024 pix.
= 41820.16 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: 40.84 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-19553.00800000000163 - 65358.5
Average (Standard dev.)64878.315999999998894 (±65.303985999999995)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-137
Dimensions10241024197
Spacing10241024197
CellA: 41820.16 Å / B: 41820.16 Å / C: 8045.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : WI-38 fibroblast

EntireName: WI-38 fibroblast
Components
  • Cell: WI-38 fibroblast

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Supramolecule #1: WI-38 fibroblast

SupramoleculeName: WI-38 fibroblast / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Tissue: Skin

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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: DMEM growth media
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 310.15 K / Instrument: LEICA EM GP
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Home made / Diameter: 15 nm

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: OTHER / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Average electron dose: 1.05 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus min: 0.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.0 µm / Nominal defocus min: 0.0 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware:
Namedetails
IMOD (ver. 4.12.10)
PRIISM/IVE (ver. 4.7.2)Deconvolved using core2_decon

Number images used: 61

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