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- EMDB-54280: Cryo-electron tomogram of apoptosis-induced HeLa cell expressing ... -

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Basic information

Entry
Database: EMDB / ID: EMD-54280
TitleCryo-electron tomogram of apoptosis-induced HeLa cell expressing Apaf1-SNAP
Map dataCryo-electron tomogram of apoptosis-induced HeLa cell expressing Apaf1-SNAP
Sample
  • Cell: HeLa cell expressing Apaf1-SNAP, treated with ABT-737 and QVD
KeywordsApoptosome / Caspase-activation / HeLa cell / APOPTOSIS
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsBorgeaud AC / Ganeva I / Klein C / Stooss A / Ross-Kaschitza D / Wu L / Riley JS / Tait SWG / Lemmin T / Kaufmann T / Kukulski W
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Nat Commun / Year: 2025
Title: Large transient assemblies of Apaf1 constitute the apoptosome in cells.
Authors: Alicia C Borgeaud / Iva Ganeva / Calvin Klein / Amandine Stooss / Daniela Ross-Kaschitza / Liyang Wu / Joel S Riley / Stephen W G Tait / Thomas Lemmin / Thomas Kaufmann / Wanda Kukulski /
Abstract: Upon cell death signals, the apoptotic protease-activating factor Apaf1 and cytochrome c interact to form the apoptosome complex. The apoptosome is crucial for mitochondrial apoptosis, as it ...Upon cell death signals, the apoptotic protease-activating factor Apaf1 and cytochrome c interact to form the apoptosome complex. The apoptosome is crucial for mitochondrial apoptosis, as it activates caspases that dismantle the cell. However, the in vivo assembly mechanism and appearance of the apoptosome remain unclear. We show that upon onset of apoptosis, Apaf1 molecules accumulate into multiple foci per cell. Disassembly of the foci correlates with cell survival. Structurally, Apaf1 foci resemble organelle-sized, cloud-like assemblies. They form through specific interactions with cytochrome c, contain caspase-9, and depend on procaspase-9 expression for their formation. We propose that Apaf1 foci correspond to the apoptosome in cells. Transientness and ultrastructure of Apaf1 foci suggest that the dynamic spatiotemporal organisation of apoptosome components regulates progression of apoptosis.
History
DepositionJul 6, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54280.png

Downloads & links

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Map

FileDownload / File: emd_54280.map.gz / Format: CCP4 / Size: 103.4 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationCryo-electron tomogram of apoptosis-induced HeLa cell expressing Apaf1-SNAP
Voxel sizeX=Y=Z: 17.82 Å
Density
Minimum - Maximum-31.0 - 20.0
Average (Standard dev.)-0.45616797 (±2.0798166)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-129
Dimensions682682233
Spacing682682233
CellA: 12153.24 Å / B: 12153.24 Å / C: 4152.06 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : HeLa cell expressing Apaf1-SNAP, treated with ABT-737 and QVD

EntireName: HeLa cell expressing Apaf1-SNAP, treated with ABT-737 and QVD
Components
  • Cell: HeLa cell expressing Apaf1-SNAP, treated with ABT-737 and QVD

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Supramolecule #1: HeLa cell expressing Apaf1-SNAP, treated with ABT-737 and QVD

SupramoleculeName: HeLa cell expressing Apaf1-SNAP, treated with ABT-737 and QVD
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
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 1 / Focused ion beam - Duration: 2000 / Focused ion beam - Temperature: 80 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: Rough milling started at 30 kV and 1 nA current, progressively lowered to final 23 pA at 16 kV for fine milling.. The value given for _em_focused_ion_beam.instrument is ...Focused ion beam - Details: Rough milling started at 30 kV and 1 nA current, progressively lowered to final 23 pA at 16 kV for fine milling.. The value given for _em_focused_ion_beam.instrument is TFS Aquilos 2. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 5.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 117
CTF correctionType: PHASE FLIPPING ONLY

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