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- EMDB-54281: Electron tomogram of resin-embedded, apoptosis-induced HeLa cell ... -

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Basic information

Entry
Database: EMDB / ID: EMD-54281
TitleElectron tomogram of resin-embedded, apoptosis-induced HeLa cell expressing Apaf1-GFP
Map dataElectron tomogram of resin-embedded, apoptosis-induced HeLa cell expressing Apaf1-GFP
Sample
  • Cell: HeLa cell expressing Apaf1-GFP, treated with ABT-737 and QVD
KeywordsApoptosome / Caspase-activation / APOPTOSIS
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM / negative staining
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_54281.png

Downloads & links

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Map

FileDownload / File: emd_54281.map.gz / Format: CCP4 / Size: 117 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationElectron tomogram of resin-embedded, apoptosis-induced HeLa cell expressing Apaf1-GFP
Voxel sizeX=Y=Z: 22.04 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)54.048169999999999 (±10.419112999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-58
Dimensions10241024117
Spacing10241024117
CellA: 22568.96 Å / B: 22568.96 Å / C: 2578.6802 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-GFP, treated with ABT-737 and QVD

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

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

SupramoleculeName: HeLa cell expressing Apaf1-GFP, 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

Methodnegative staining, cryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7
StainingType: NEGATIVE / Material: Uranyl acetate
Sugar embeddingMaterial: Lowicryl HM20
VitrificationCryogen name: NITROGEN
DetailsCells grown on sapphire disks, high-pressure frozen and freeze-substituted
High pressure freezingInstrument: OTHER
Details: The value given for _em_high_pressure_freezing.instrument is Leica HPM100. This is not in a list of allowed values {'EMS-002 RAPID IMMERSION FREEZER', 'LEICA EM HPM100', 'OTHER', 'BAL-TEC ...Details: The value given for _em_high_pressure_freezing.instrument is Leica HPM100. This is not in a list of allowed values {'EMS-002 RAPID IMMERSION FREEZER', 'LEICA EM HPM100', 'OTHER', 'BAL-TEC HPM 010', 'LEICA EM PACT2', 'LEICA EM PACT'} so OTHER is written into the XML file.
SectioningUltramicrotomy - Instrument: Leica / Ultramicrotomy - Temperature: 293 K / Ultramicrotomy - Final thickness: 300
Fiducial markerManufacturer: Agar Scientific / Diameter: 15 nm

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Electron microscopy

MicroscopeFEI TECNAI F20
DetailsSTEM mode on an axial brightfield detector
Image recordingFilm or detector model: OTHER / Average electron dose: 1000.0 e/Å2
Details: ET was done in STEM mode on an axial brightfield detector with a high-tilt tomography holder at 1.102 nm pixel size with a camera length of 200 mm. [NOTE: Electron dose unknown. Value specified here is a dummy]
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.0 µm / Nominal defocus min: 0.0 µm
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 242
CTF correctionType: NONE

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