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Yorodumi- EMDB-11417: Tomogram of endogenous a-synuclein inclusion in primary mouse neu... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11417 | |||||||||
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Title | Tomogram of endogenous a-synuclein inclusion in primary mouse neurons seeded with PFFs | |||||||||
Map data | Tomogram of endogenous a-synuclein aggregate in primary mouse neurons seeded with PFFs | |||||||||
Sample |
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Biological species | Mus musculus (house mouse) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Trinkaus VA / Hartl FU / Fernandez-Busnadiego R | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Nat Commun / Year: 2021 Title: In situ architecture of neuronal α-Synuclein inclusions. Authors: Victoria A Trinkaus / Irene Riera-Tur / Antonio Martínez-Sánchez / Felix J B Bäuerlein / Qiang Guo / Thomas Arzberger / Wolfgang Baumeister / Irina Dudanova / Mark S Hipp / F Ulrich Hartl ...Authors: Victoria A Trinkaus / Irene Riera-Tur / Antonio Martínez-Sánchez / Felix J B Bäuerlein / Qiang Guo / Thomas Arzberger / Wolfgang Baumeister / Irina Dudanova / Mark S Hipp / F Ulrich Hartl / Rubén Fernández-Busnadiego / Abstract: The molecular architecture of α-Synuclein (α-Syn) inclusions, pathognomonic of various neurodegenerative disorders, remains unclear. α-Syn inclusions were long thought to consist mainly of α-Syn ...The molecular architecture of α-Synuclein (α-Syn) inclusions, pathognomonic of various neurodegenerative disorders, remains unclear. α-Syn inclusions were long thought to consist mainly of α-Syn fibrils, but recent reports pointed to intracellular membranes as the major inclusion component. Here, we use cryo-electron tomography (cryo-ET) to image neuronal α-Syn inclusions in situ at molecular resolution. We show that inclusions seeded by α-Syn aggregates produced recombinantly or purified from patient brain consist of α-Syn fibrils crisscrossing a variety of cellular organelles. Using gold-labeled seeds, we find that aggregate seeding is predominantly mediated by small α-Syn fibrils, from which cytoplasmic fibrils grow unidirectionally. Detailed analysis of membrane interactions revealed that α-Syn fibrils do not contact membranes directly, and that α-Syn does not drive membrane clustering. Altogether, we conclusively demonstrate that neuronal α-Syn inclusions consist of α-Syn fibrils intermixed with membranous organelles, and illuminate the mechanism of aggregate seeding and cellular interaction. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11417.map.gz | 694.4 MB | EMDB map data format | |
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Header (meta data) | emd-11417-v30.xml emd-11417.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | emd_11417.png | 416.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11417 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11417 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_11417.map.gz / Format: CCP4 / Size: 752.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Tomogram of endogenous a-synuclein aggregate in primary mouse neurons seeded with PFFs | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : Endogenous alpha-synuclein inclusion in primary mouse neuron seed...
Entire | Name: Endogenous alpha-synuclein inclusion in primary mouse neuron seeded with PFFs |
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Components |
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-Supramolecule #1: Endogenous alpha-synuclein inclusion in primary mouse neuron seed...
Supramolecule | Name: Endogenous alpha-synuclein inclusion in primary mouse neuron seeded with PFFs type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/4 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 80 % / Chamber temperature: 310 K / Instrument: FEI VITROBOT MARK IV |
Cryo protectant | 10 % Glycerol |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.1 nA / Focused ion beam - Duration: 2400 sec. / Focused ion beam - Temperature: 77 K / Focused ion beam - Initial thickness: 1000 nm / Focused ion beam - Final thickness: 150 nm Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Quanta FIB. This is not in a list of allowed values {'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: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 7.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 34000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Temperature | Min: 70.0 K / Max: 75.0 K |
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 / Digitization - Frames/image: 17-24 / Number grids imaged: 1 / Number real images: 55 / Average exposure time: 2.55 sec. / Average electron dose: 2.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.9.0) / Number images used: 56 |
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