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- EMDB-51759: Dual-Axis cryo-STEM tomogram of a Mitochondrion from MFF-/- MEFs -

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Basic information

Entry
Database: EMDB / ID: EMD-51759
TitleDual-Axis cryo-STEM tomogram of a Mitochondrion from MFF-/- MEFs
Map dataDual-axis BF-STEM cryo-Tomogram of MFF-/- MEFs
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
Citation
Journal: J Cell Sci / Year: 2025
Title: Snapshots of mitochondrial fission imaged by cryo-scanning transmission electron tomography.
Authors: Peter Kirchweger / Sharon Grayer Wolf / Neta Varsano / Tali Dadosh / Guenter P Resch / Michael Elbaum /
Abstract: Mitochondria undergo constant remodeling via fission, fusion, extension and degradation. Fission, in particular, depends on the accumulation of mitochondrial fission factor (MFF) and subsequent ...Mitochondria undergo constant remodeling via fission, fusion, extension and degradation. Fission, in particular, depends on the accumulation of mitochondrial fission factor (MFF) and subsequent recruitment of the dynamin-related protein DRP1 (also known as DNM1L). We used cryo-scanning transmission electron tomography (cryo-STET) to investigate mitochondrial morphologies in MFF mutant (MFF-/-) mouse embryonic fibroblast (MEF) cells in ATP-depleting conditions that normally induce fission. The capability of cryo-STET to image through the cytoplasmic volume to a depth of 1 µm facilitated visualization of intact mitochondria and their surroundings. We imaged changes in mitochondrial morphology and cristae structure, as well as contacts with the endoplasmic reticulum (ER), degradative organelles and the cytoskeleton at stalled fission sites. We found disruption of the outer mitochondrial membrane at contact sites with the ER and degradative organelles at sites of mitophagy. We identified fission sites where the inner mitochondrial membrane is already separated while the outer membrane is still continuous. Although MFF is a general fission factor, these observations demonstrate that mitochondrial fission can proceed to the final stage in its absence. The use of cryo-STET allays concerns about the loss of structures due to sample thinning required for tomography using cryo-transmission electron microscopy.
#1: Journal: 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-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51759.png

Downloads & links

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Map

FileDownload / File: emd_51759.map.gz / Format: CCP4 / Size: 5.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDual-axis BF-STEM cryo-Tomogram of MFF-/- MEFs
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
20.42 Å/pix.
x 349 pix.
= 7126.58 Å		20.42 Å/pix.
x 2048 pix.
= 41820.16 Å		20.42 Å/pix.
x 2048 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: 20.42 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-137489.799999999988358 - 8585814.0
Average (Standard dev.)4279.332000000000335 (±1260.895800000000008)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-163
Dimensions20482048349
Spacing20482048349
CellA: 41820.16 Å / B: 41820.16 Å / C: 7126.58 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 deletion MEF, expressing a mito-GFP
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: 4096 pixel / Digitization - Dimensions - Height: 4096 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: 41000
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: 122
CTF correctionDetails: CSTET needs no CTF correction / Type: NONE

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