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- EMDB-53409: The targeting of non-fibrillar polyQ via distinct VCP-proteasome ... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-53409
TitleThe targeting of non-fibrillar polyQ via distinct VCP-proteasome coupling
Map data20S proteasome, D7
Sample
  • Cell: Neuro2a expressing Q150-GFP aggregate
Keywordsproteasome 20S / D7 / CHAPERONE
Biological speciesmouse (mice)
Methodsubtomogram averaging / cryo EM / Resolution: 10.0 Å
AuthorsZhao DY
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: bioRxiv
Title: The targeting of non-fibrillar polyQ via distinct VCP-proteasome coupling
Authors: Zhao DY
History
DepositionApr 12, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53409.png

Downloads & links

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Map

FileDownload / File: emd_53409.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation20S proteasome, D7
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.78 Å/pix.
x 80 pix.
= 302.4 Å		3.78 Å/pix.
x 80 pix.
= 302.4 Å		3.78 Å/pix.
x 80 pix.
= 302.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.78 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.72462916 - 0.8362211
Average (Standard dev.)0.006480766 (±0.06071663)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 302.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_53409_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53409_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Neuro2a expressing Q150-GFP aggregate

EntireName: Neuro2a expressing Q150-GFP aggregate
Components
  • Cell: Neuro2a expressing Q150-GFP aggregate

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Supramolecule #1: Neuro2a expressing Q150-GFP aggregate

SupramoleculeName: Neuro2a expressing Q150-GFP aggregate / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: mouse (mice)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 50 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 80.0 K / Max: 100.0 K
DetailsFor dataset 2, 410 tilt series were collected on a Titan Krios G4 instrument at 300 kV equipped with a Selectris X energy filter operating at zero-loss with a slit width of 10 eV, and a Falcon 4i camera (Thermo). Low-magnification images were taken at 11500x (object pixel size 2.13 nm) to generate lamella overviews. Tilt series were recorded at 1.89 A pixel size using the Tomography 5 (Thermo) in EER file format, with a dose-symmetric tilt scheme. The tilt series were collected with a 3 degree tilt increment with an angular range of ~120 degrees, and with cumulative dose of 80-120 electrons/A^2. Targeted defocus was in the range of -5 to -3 um.
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average exposure time: 1.0 sec. / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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

DetailsRaw frames were pre-processed using in-house Matlab wrapper scripts (Tomoman: https://github.com/williamnwan/TOMOMAN). The relative shifts of the image between camera frames due to stage drift and beam-induced motion were corrected by MotionCor2, followed by exposure filtering. The EER frames were motion corrected using Relion's implementation of MotionCor2 followed by exposure filtering. Bad tilts were removed upon manual inspection using the Tomoman script. The tilt series were then aligned using patch tracking, binned, and reconstructed by weighted back projection in IMOD. CTF was estimated by tiltCTF and the final CTF-corrected reconstruction was made in IMOD for template matching. For figure display, tomogram contrast was enhanced upon denoising with cryoCARE, by which tilt series were separated into odd and even tilts during motion correction.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number subtomograms used: 16146
ExtractionNumber tomograms: 410 / Number images used: 16146 / Software - Name: Warp (ver. 1.0.9)
CTF correctionType: NONE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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