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- EMDB-18896: Lipophagy in 5-day starved WT yeast cell. -

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Basic information

Entry
Database: EMDB / ID: EMD-18896
TitleLipophagy in 5-day starved WT yeast cell.
Map dataLipophagy in 5-day starved WT yeast cell.
Sample
  • Cell: Lipid droplet-vacuole contact site
KeywordsLipid droplet / vacuole / membrane contact site. / MEMBRANE PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodelectron tomography / cryo EM
AuthorsCollado J
Funding support Germany, Austria, 5 items
OrganizationGrant numberCountry
Gerty Cori Programme, Medical Faculty, University of MunsterEXC 1003 - CiM Germany
German Research Foundation (DFG)264061860 Germany
Germanys Excellence StrategyEXC 2067/1-390729940 Germany
German Research Foundation (DFG)448415290 Germany
Austrian Science FundP36187-B Austria
CitationJournal: Dev Cell / Year: 2024
Title: A metabolically controlled contact site between vacuoles and lipid droplets in yeast.
Authors: Duy Trong Vien Diep / Javier Collado / Marie Hugenroth / Rebecca Martina Fausten / Louis Percifull / Mike Wälte / Christian Schuberth / Oliver Schmidt / Rubén Fernández-Busnadiego / Maria Bohnert /
Abstract: The lipid droplet (LD) organization proteins Ldo16 and Ldo45 affect multiple aspects of LD biology in yeast. They are linked to the LD biogenesis machinery seipin, and their loss causes defects in LD ...The lipid droplet (LD) organization proteins Ldo16 and Ldo45 affect multiple aspects of LD biology in yeast. They are linked to the LD biogenesis machinery seipin, and their loss causes defects in LD positioning, protein targeting, and breakdown. However, their molecular roles remained enigmatic. Here, we report that Ldo16/45 form a tether complex with Vac8 to create vacuole lipid droplet (vCLIP) contact sites, which can form in the absence of seipin. The phosphatidylinositol transfer protein (PITP) Pdr16 is a further vCLIP-resident recruited specifically by Ldo45. While only an LD subpopulation is engaged in vCLIPs at glucose-replete conditions, nutrient deprivation results in vCLIP expansion, and vCLIP defects impair lipophagy upon prolonged starvation. In summary, Ldo16/45 are multifunctional proteins that control the formation of a metabolically regulated contact site. Our studies suggest a link between LD biogenesis and breakdown and contribute to a deeper understanding of how lipid homeostasis is maintained during metabolic challenges.
History
DepositionNov 15, 2023-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18896.png

Downloads & links

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Map

FileDownload / File: emd_18896.map.gz / Format: CCP4 / Size: 768 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLipophagy in 5-day starved WT yeast cell.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
14.6 Å/pix.
x 192 pix.
= 2803.2 Å		14.6 Å/pix.
x 1024 pix.
= 14950.4 Å		14.6 Å/pix.
x 1024 pix.
= 14950.4 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 14.6 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-11.626374 - 5.28473
Average (Standard dev.)0.14826486 (±0.41889462)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-95
Dimensions10241024192
Spacing10241024192
CellA: 14950.4 Å / B: 14950.4 Å / C: 2803.2002 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-vacuole contact site

EntireName: Lipid droplet-vacuole contact site
Components
  • Cell: Lipid droplet-vacuole contact site

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Supramolecule #1: Lipid droplet-vacuole contact site

SupramoleculeName: Lipid droplet-vacuole contact site / 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: 6.5
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 80 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV / Details: Back-blotted.
DetailsCells were plunge-frozen at 0.6 O.D600 concentration.
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.1 / Focused ion beam - Duration: 1000 / Focused ion beam - Temperature: 78 K / Focused ion beam - Initial thickness: 4000 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Thermo Fisher Aquilos 2 FIB. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 6.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 33000
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 80.0 K / Max: 80.0 K
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average exposure time: 2.8 sec. / Average electron dose: 3.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 36

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