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- EMDB-18115: phagophore and lysosomes with amorphous polyQ -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-18115
Titlephagophore and lysosomes with amorphous polyQ
Map dataautolysosome and lysosomes next to fibrillar polyQ Q97
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: To Be Published
Title: Autophagy preferentially degrades non-fibrillar polyQ aggregates
Authors: Zhao DY / Bauerlein FJB / Saha I / Hartl FU / Baumeister W / Wilfling F
History
DepositionAug 2, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18115.png

Downloads & links

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Map

FileDownload / File: emd_18115.map.gz / Format: CCP4 / Size: 180.1 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Annotationautolysosome and lysosomes next to fibrillar polyQ Q97
Voxel sizeX=Y=Z: 26 Å
Density
Minimum - Maximum-785.0 - 432.0
Average (Standard dev.)7.3441916 (±26.454542)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions960928106
Spacing928960106
CellA: 24128.0 Å / B: 24960.0 Å / C: 2756.0 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 POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 18000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 50

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