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Yorodumi- EMDB-18117: autophagosome and autolysosomes are empty next to fibrillar polyQ -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18117 | |||||||||
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Title | autophagosome and autolysosomes are empty next to fibrillar polyQ | |||||||||
Map data | autophagosome and autolysosome are empty next to polyQ fibrils | |||||||||
Sample |
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Keywords | poly-glutamine / neurodegeneration / PROTEIN FIBRIL | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Zhao DY | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18117.map.gz | 92.7 MB | EMDB map data format | |
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Header (meta data) | emd-18117-v30.xml emd-18117.xml | 7.6 KB 7.6 KB | Display Display | EMDB header |
Images | emd_18117.png | 31.4 KB | ||
Filedesc metadata | emd-18117.cif.gz | 3.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18117 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18117 | HTTPS FTP |
-Validation report
Summary document | emd_18117_validation.pdf.gz | 454.3 KB | Display | EMDB validaton report |
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Full document | emd_18117_full_validation.pdf.gz | 453.8 KB | Display | |
Data in XML | emd_18117_validation.xml.gz | 7 KB | Display | |
Data in CIF | emd_18117_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18117 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18117 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_18117.map.gz / Format: CCP4 / Size: 169.9 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||
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Annotation | autophagosome and autolysosome are empty next to polyQ fibrils | ||||||||||||||||||||
Voxel size | X=Y=Z: 26 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Hek293 expressing polyQ-GFP
Entire | Name: Hek293 expressing polyQ-GFP |
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Components |
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-Supramolecule #1: Hek293 expressing polyQ-GFP
Supramolecule | Name: Hek293 expressing polyQ-GFP / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
Sectioning | Focused 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. |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Final reconstruction | Number images used: 50 |
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