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Yorodumi- EMDB-4191: In situ cryo-electron tomogram from Rat neuron with C9ORF72 Poly-... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4191 | |||||||||
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Title | In situ cryo-electron tomogram from Rat neuron with C9ORF72 Poly-GA aggregates | |||||||||
Map data | Tomogram of Rat neuron cell | |||||||||
Sample |
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Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Guo Q / Lehmer C / Martinez-Sanchez A / Rudack T / Beck F / Hartmann H / Hipp MS / Hartl FU / Edbauer D / Baumeister W / Fernandez-Busnadiego F | |||||||||
Citation | Journal: Cell / Year: 2018 Title: In Situ Structure of Neuronal C9orf72 Poly-GA Aggregates Reveals Proteasome Recruitment. Authors: Qiang Guo / Carina Lehmer / Antonio Martínez-Sánchez / Till Rudack / Florian Beck / Hannelore Hartmann / Manuela Pérez-Berlanga / Frédéric Frottin / Mark S Hipp / F Ulrich Hartl / ...Authors: Qiang Guo / Carina Lehmer / Antonio Martínez-Sánchez / Till Rudack / Florian Beck / Hannelore Hartmann / Manuela Pérez-Berlanga / Frédéric Frottin / Mark S Hipp / F Ulrich Hartl / Dieter Edbauer / Wolfgang Baumeister / Rubén Fernández-Busnadiego / Abstract: Protein aggregation and dysfunction of the ubiquitin-proteasome system are hallmarks of many neurodegenerative diseases. Here, we address the elusive link between these phenomena by employing cryo- ...Protein aggregation and dysfunction of the ubiquitin-proteasome system are hallmarks of many neurodegenerative diseases. Here, we address the elusive link between these phenomena by employing cryo-electron tomography to dissect the molecular architecture of protein aggregates within intact neurons at high resolution. We focus on the poly-Gly-Ala (poly-GA) aggregates resulting from aberrant translation of an expanded GGGGCC repeat in C9orf72, the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. We find that poly-GA aggregates consist of densely packed twisted ribbons that recruit numerous 26S proteasome complexes, while other macromolecules are largely excluded. Proximity to poly-GA ribbons stabilizes a transient substrate-processing conformation of the 26S proteasome, suggesting stalled degradation. Thus, poly-GA aggregates may compromise neuronal proteostasis by driving the accumulation and functional impairment of a large fraction of cellular proteasomes. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4191.map.gz | 215.5 MB | EMDB map data format | |
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Header (meta data) | emd-4191-v30.xml emd-4191.xml | 14.9 KB 14.9 KB | Display Display | EMDB header |
Images | emd_4191.png | 75.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4191 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4191 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4191.map.gz / Format: CCP4 / Size: 232.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Tomogram of Rat neuron cell | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 13.68 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 : in situ tomogram from Rat neuron
Entire | Name: in situ tomogram from Rat neuron |
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Components |
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-Supramolecule #1: in situ tomogram from Rat neuron
Supramolecule | Name: in situ tomogram from Rat neuron / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1-#32 |
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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 | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: The grid was coated with C prior to use |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
Details | FIB milled rat primary neurons |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.5 nA / Focused ion beam - Dose rate: 1 / Focused ion beam - Duration: 100 sec. / Focused ion beam - Temperature: 90 K / Focused ion beam - Initial thickness: 1500 / Focused ion beam - Final thickness: 200 Focused ion beam - Details: 11nA rough milling. The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Scios. This is not in a list of allowed values set(['DB235', 'OTHER']) so OTHER ...Focused ion beam - Details: 11nA rough milling. The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Scios. This is not in a list of allowed values set(['DB235', 'OTHER']) so OTHER is written into the XML file. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 7.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 42000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average exposure time: 2.0 sec. / Average electron dose: 1.8 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution method: OTHER / Software - Name: eTomo / Number images used: 59 |
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