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- EMDB-51761: Cryo-STEM tomogram of a Mitochondrion from MFF-/- MEFs under fiss... -

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Basic information

Entry
Database: EMDB / ID: EMD-51761
TitleCryo-STEM tomogram of a Mitochondrion from MFF-/- MEFs under fission inducing conditions
Map dataCSTET tomogram of MFF-/- MEF cell under fission inducing conditions
Sample
  • Cell: Mouse embryonic fibroblast
KeywordsMitochondrial morphology / whole cell tomography / cryo-STEM Tomography / CSTET / UNKNOWN FUNCTION
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsKirchweger P / Wolf SG / Elbaum M / Fass D
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: Biorxiv / Year: 2024
Title: Snapshots of Mitochondrial Fission Imaged by Cryo-Scanning Transmission Electron Tomography
Authors: Kirchweger P / Wolf SG / Varsano N / Dadosh T / Resch GP / Elbaum M
History
DepositionOct 9, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51761.png

Downloads & links

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Map

FileDownload / File: emd_51761.map.gz / Format: CCP4 / Size: 4.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCSTET tomogram of MFF-/- MEF cell under fission inducing conditions
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
30.01 Å/pix.
x 296 pix.
= 8881.646 Å		30.01 Å/pix.
x 2048 pix.
= 61451.391 Å		30.01 Å/pix.
x 2048 pix.
= 61451.391 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: 30.00556 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-10841.091000000000349 - 14815902.0
Average (Standard dev.)3901.014999999999873 (±1150.865500000000111)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-1314-132
Dimensions20482048296
Spacing20482048296
CellA: 61451.39 Å / B: 61451.39 Å / C: 8881.646 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Mouse embryonic fibroblast

EntireName: Mouse embryonic fibroblast
Components
  • Cell: Mouse embryonic fibroblast

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Supramolecule #1: Mouse embryonic fibroblast

SupramoleculeName: Mouse embryonic fibroblast / type: cell / ID: 1 / Parent: 0
Details: Mitochondrial fission factor (MFF) deletion MEF, expressing a mito-GFP, 10 uM Oligomycin
Source (natural)Organism: Mus musculus (house mouse)

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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
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR
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
Details: Images were recorded on a Fischione HAADF detector in BrightField mode (described in Kirchweger et al., 2023).
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 reconstructionAlgorithm: BACK PROJECTION
Software:
Namedetails
IMOD (ver. 4.12.10)
PRIISM/IVE (ver. 4.7.2)Deconvolved using core2_decon

Details: After WBP, the tomogram was deconvolved as described in Waugh et al. (2021) and Kirchweger et al. (2023)
Number images used: 61

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