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- EMDB-24764: in situ cryo-electron tomogram of wild-type yeast lipid droplet a... -

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Basic information

Entry
Database: EMDB / ID: EMD-24764
Titlein situ cryo-electron tomogram of wild-type yeast lipid droplet after 4-hour exposure to acute glucose restriction (AGR, 0.001% glucose media)
Map data
Sample
  • Cell: lipid droplet of wild-type yeast after 4-hour exposure to acute glucose restriction (AGR, 0.001% glucose media)
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodelectron tomography / cryo EM
AuthorsRogers S / Gui L / Kovalenko A / Reetz E / Nicastro D / Henne WM
Funding support United States, 4 items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RR140082 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM119768 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK126887 United States
Welch FoundationI-1873 United States
CitationJournal: 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
DepositionAug 27, 2021-
Header (metadata) releaseSep 14, 2022-
Map releaseSep 14, 2022-
UpdateSep 14, 2022-
Current statusSep 14, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24764.png

Downloads & links

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Map

FileDownload / File: emd_24764.map.gz / Format: CCP4 / Size: 183.4 MB / Type: IMAGE STORED AS SIGNED BYTE
Voxel sizeX=Y=Z: 5.684 Å
Density
Minimum - Maximum-71.0 - 42.0
Average (Standard dev.)-3.7579405 (±6.951076)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-648-2605250
Dimensions599642500
Spacing642599500
CellA: 3649.128 Å / B: 3404.716 Å / C: 2842.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : lipid droplet of wild-type yeast after 4-hour exposure to acute g...

EntireName: lipid droplet of wild-type yeast after 4-hour exposure to acute glucose restriction (AGR, 0.001% glucose media)
Components
  • Cell: lipid droplet of wild-type yeast after 4-hour exposure to acute glucose restriction (AGR, 0.001% glucose media)

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Supramolecule #1: lipid droplet of wild-type yeast after 4-hour exposure to acute g...

SupramoleculeName: lipid droplet of wild-type yeast after 4-hour exposure to acute glucose restriction (AGR, 0.001% glucose media)
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE
SectioningFocused 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.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 57

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