+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18110 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The fibrillar and amorphous states of polyQ Q97 | |||||||||
Map data | The fibrillar and amorphous states of polyQ Q97 | |||||||||
Sample |
| |||||||||
Keywords | polyQ aggregates / neurodegeneration / PROTEIN FIBRIL | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Zhao DY | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: To Be Published Title: Autophagy preferentially degrades non-fibrillar polyQ aggregates Authors: Zhao DY / Bauerlein FJB / Saha I / Hartl FU / Baumeister W / Wilfling F | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_18110.map.gz | 1.4 GB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-18110-v30.xml emd-18110.xml | 8.3 KB 8.3 KB | Display Display | EMDB header |
Images | emd_18110.png | 255 KB | ||
Filedesc metadata | emd-18110.cif.gz | 3.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18110 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18110 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_18110.map.gz / Format: CCP4 / Size: 1.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | The fibrillar and amorphous states of polyQ Q97 | ||||||||||||||||||||
Voxel size | X=Y=Z: 12.76 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Sample components
-Entire : polyQ aggregates in Hek293 cells
Entire | Name: polyQ aggregates in Hek293 cells |
---|---|
Components |
|
-Supramolecule #1: polyQ aggregates in Hek293 cells
Supramolecule | Name: polyQ aggregates in Hek293 cells / type: cell / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 / Details: Cell media with 10% glycerol |
---|---|
Grid | Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 25 % / Chamber temperature: 298 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 / 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. 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 |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm |
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 / Average electron dose: 2.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Number images used: 50 |
---|