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Yorodumi- EMDB-24762: in situ cryo-electron tomogram of wild-type yeast lipid droplet i... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24762 | |||||||||||||||
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Title | in situ cryo-electron tomogram of wild-type yeast lipid droplet in 2% glucose-fed log growth conditions | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||
Method | electron tomography / cryo EM | |||||||||||||||
Authors | Rogers S / Gui L / Kovalenko A / Reetz E / Nicastro D / Henne WM | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: To Be Published Title: Liquid-crystalline lipid phase transitions in lipid droplets selectively remodel the LD proteome Authors: Rogers S / Gui L / Kovalenko A / Reetz E / Nicastro D / Henne WM | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_24762.map.gz | 104.1 MB | EMDB map data format | |
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Header (meta data) | emd-24762-v30.xml emd-24762.xml | 8.1 KB 8.1 KB | Display Display | EMDB header |
Images | emd_24762.png | 169.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24762 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24762 | HTTPS FTP |
-Validation report
Summary document | emd_24762_validation.pdf.gz | 571.1 KB | Display | EMDB validaton report |
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Full document | emd_24762_full_validation.pdf.gz | 570.7 KB | Display | |
Data in XML | emd_24762_validation.xml.gz | 3.2 KB | Display | |
Data in CIF | emd_24762_validation.cif.gz | 3.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24762 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24762 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_24762.map.gz / Format: CCP4 / Size: 242.8 MB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||
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Voxel size | X=Y=Z: 5.684 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : lipid droplet of wild-type yeast in 2% glucose-fed log growth con...
Entire | Name: lipid droplet of wild-type yeast in 2% glucose-fed log growth conditions |
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Components |
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-Supramolecule #1: lipid droplet of wild-type yeast in 2% glucose-fed log growth con...
Supramolecule | Name: lipid droplet of wild-type yeast in 2% glucose-fed log growth conditions type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-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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Vitrification | Cryogen name: ETHANE |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.01 nA / Focused ion beam - Duration: 600 sec. / Focused ion beam - Temperature: 88 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 Aquilos. 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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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.5 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 | Number images used: 57 |
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