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- EMDB-18114: phagophore in fibrillar polyQ -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-18114
Titlephagophore in fibrillar polyQ
Map dataphagphore with fibrillar polyQ
Sample
  • Cell: polyQ aggregates in Hek293 cells
KeywordspolyQ aggregates / 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_18114.png

Downloads & links

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Map

FileDownload / File: emd_18114.map.gz / Format: CCP4 / Size: 446.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationphagphore with fibrillar polyQ
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
12.76 Å/pix.
x 136 pix.
= 1735.36 Å		12.76 Å/pix.
x 928 pix.
= 11841.28 Å		12.76 Å/pix.
x 928 pix.
= 11841.28 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: 12.76 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-54.515970000000003 - 24.257041999999998
Average (Standard dev.)0.009960123 (±0.5021125)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions928928136
Spacing928928136
CellA: 11841.28 Å / B: 11841.28 Å / C: 1735.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : polyQ aggregates in Hek293 cells

EntireName: polyQ aggregates in Hek293 cells
Components
  • Cell: polyQ aggregates in Hek293 cells

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Supramolecule #1: polyQ aggregates in Hek293 cells

SupramoleculeName: polyQ aggregates in Hek293 cells / 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 / Details: Cell media with 10% glycerol
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 25 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
Cryo protectant10% glycerol
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. 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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / 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: 3.0 µm
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 reconstructionNumber images used: 50

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