+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32217 | |||||||||
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Title | tomogram of a rat primary neuron harboring TDP-25 inclusion | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Guo Q | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: EMBO Rep / Year: 2022 Title: Gel-like inclusions of C-terminal fragments of TDP-43 sequester stalled proteasomes in neurons. Authors: Henrick Riemenschneider / Qiang Guo / Jakob Bader / Frédéric Frottin / Daniel Farny / Gernot Kleinberger / Christian Haass / Matthias Mann / F Ulrich Hartl / Wolfgang Baumeister / Mark S ...Authors: Henrick Riemenschneider / Qiang Guo / Jakob Bader / Frédéric Frottin / Daniel Farny / Gernot Kleinberger / Christian Haass / Matthias Mann / F Ulrich Hartl / Wolfgang Baumeister / Mark S Hipp / Felix Meissner / Rubén Fernández-Busnadiego / Dieter Edbauer / Abstract: Aggregation of the multifunctional RNA-binding protein TDP-43 defines large subgroups of amyotrophic lateral sclerosis and frontotemporal dementia and correlates with neurodegeneration in both ...Aggregation of the multifunctional RNA-binding protein TDP-43 defines large subgroups of amyotrophic lateral sclerosis and frontotemporal dementia and correlates with neurodegeneration in both diseases. In disease, characteristic C-terminal fragments of ~25 kDa ("TDP-25") accumulate in cytoplasmic inclusions. Here, we analyze gain-of-function mechanisms of TDP-25 combining cryo-electron tomography, proteomics, and functional assays. In neurons, cytoplasmic TDP-25 inclusions are amorphous, and photobleaching experiments reveal gel-like biophysical properties that are less dynamic than nuclear TDP-43. Compared with full-length TDP-43, the TDP-25 interactome is depleted of low-complexity domain proteins. TDP-25 inclusions are enriched in 26S proteasomes adopting exclusively substrate-processing conformations, suggesting that inclusions sequester proteasomes, which are largely stalled and no longer undergo the cyclic conformational changes required for proteolytic activity. Reporter assays confirm that TDP-25 impairs proteostasis, and this inhibitory function is enhanced by ALS-causing TDP-43 mutations. These findings support a patho-physiological relevance of proteasome dysfunction in ALS/FTD. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_32217.map.gz | 150.3 MB | EMDB map data format | |
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Header (meta data) | emd-32217-v30.xml emd-32217.xml | 8.4 KB 8.4 KB | Display Display | EMDB header |
Images | emd_32217.png | 306.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32217 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32217 | HTTPS FTP |
-Validation report
Summary document | emd_32217_validation.pdf.gz | 386.2 KB | Display | EMDB validaton report |
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Full document | emd_32217_full_validation.pdf.gz | 385.8 KB | Display | |
Data in XML | emd_32217_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | emd_32217_validation.cif.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32217 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32217 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_32217.map.gz / Format: CCP4 / Size: 162.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 14.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : rat primary neuron culture with TDP-25 inclusion
Entire | Name: rat primary neuron culture with TDP-25 inclusion |
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Components |
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-Supramolecule #1: rat primary neuron culture with TDP-25 inclusion
Supramolecule | Name: rat primary neuron culture with TDP-25 inclusion / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
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Grid | Material: GOLD |
Vitrification | Cryogen name: ETHANE-PROPANE |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 1 nA / Focused ion beam - Duration: 1 sec. / Focused ion beam - Temperature: 100 K / Focused ion beam - Initial thickness: 1000 nm / Focused ion beam - Final thickness: 200 nm Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is quanta. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Number images used: 40 |
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