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- EMDB-18117: autophagosome and autolysosomes are empty next to fibrillar polyQ -

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Basic information

Entry
Database: EMDB / ID: EMD-18117
Titleautophagosome and autolysosomes are empty next to fibrillar polyQ
Map dataautophagosome and autolysosome are empty next to polyQ fibrils
Sample
  • Cell: Hek293 expressing polyQ-GFP
Keywordspoly-glutamine / neurodegeneration / PROTEIN FIBRIL
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsZhao DY
Funding support United States, 1 items
OrganizationGrant numberCountry
Michael J. Fox FoundationASAP-000282 United States
CitationJournal: Mol Cell / Year: 2024
Title: Autophagy preferentially degrades non-fibrillar polyQ aggregates.
Authors: Dorothy Y Zhao / Felix J B Bäuerlein / Itika Saha / F Ulrich Hartl / Wolfgang Baumeister / Florian Wilfling /
Abstract: Aggregation of proteins containing expanded polyglutamine (polyQ) repeats is the cytopathologic hallmark of a group of dominantly inherited neurodegenerative diseases, including Huntington's disease ...Aggregation of proteins containing expanded polyglutamine (polyQ) repeats is the cytopathologic hallmark of a group of dominantly inherited neurodegenerative diseases, including Huntington's disease (HD). Huntingtin (Htt), the disease protein of HD, forms amyloid-like fibrils by liquid-to-solid phase transition. Macroautophagy has been proposed to clear polyQ aggregates, but the efficiency of aggrephagy is limited. Here, we used cryo-electron tomography to visualize the interactions of autophagosomes with polyQ aggregates in cultured cells in situ. We found that an amorphous aggregate phase exists next to the radially organized polyQ fibrils. Autophagosomes preferentially engulfed this amorphous material, mediated by interactions between the autophagy receptor p62/SQSTM1 and the non-fibrillar aggregate surface. In contrast, amyloid fibrils excluded p62 and evaded clearance, resulting in trapping of autophagic structures. These results suggest that the limited efficiency of autophagy in clearing polyQ aggregates is due to the inability of autophagosomes to interact productively with the non-deformable, fibrillar disease aggregates.
History
DepositionAug 2, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18117.png

Downloads & links

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Map

FileDownload / File: emd_18117.map.gz / Format: CCP4 / Size: 169.9 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Annotationautophagosome and autolysosome are empty next to polyQ fibrils
Voxel sizeX=Y=Z: 26 Å
Density
Minimum - Maximum-928.0 - 392.0
Average (Standard dev.)12.08873 (±28.757861999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions960928100
Spacing928960100
CellA: 24128.0 Å / B: 24960.0 Å / C: 2600.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Hek293 expressing polyQ-GFP

EntireName: Hek293 expressing polyQ-GFP
Components
  • Cell: Hek293 expressing polyQ-GFP

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Supramolecule #1: Hek293 expressing polyQ-GFP

SupramoleculeName: Hek293 expressing polyQ-GFP / 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: 7.5
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.05 / Focused ion beam - Duration: 1800 / Focused ion beam - Temperature: 100 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 250
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is FEI FIB. 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

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 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: 4.5 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 50

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