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- EMDB-54489: Tomogram of a yeast cell treated with alpha-factor (bud region) -

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Basic information

Entry
Database: EMDB / ID: EMD-54489
TitleTomogram of a yeast cell treated with alpha-factor (bud region)
Map data
Sample
  • Cell: Tomogram of yeast cell overexpressing Ldm1, treated with alpha-factor (unbudded region)
Keywordsmyosin-adaptor / lipid droplet motility / CYTOSOLIC PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodelectron tomography / cryo EM
AuthorsKeller J / Diep DTV / Zhao X-T / Bohnert M / Fernandez-Busnadiego R
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1190 Germany
CitationJournal: Cell Rep / Year: 2025
Title: The Myo2 adaptor Ldm1 and its receptor Ldo16 mediate actin-dependent lipid droplet motility.
Authors: Xue-Tong Zhao / Duy Trong Vien Diep / Louis Percifull / Rebecca Martina Fausten / Marie Hugenroth / Pascal Höhne / Beatriz Leite / Bianca Marie Esch / Javier Collado / Jenny Keller / ...Authors: Xue-Tong Zhao / Duy Trong Vien Diep / Louis Percifull / Rebecca Martina Fausten / Marie Hugenroth / Pascal Höhne / Beatriz Leite / Bianca Marie Esch / Javier Collado / Jenny Keller / Stephan Wilmes / Meryem Aysenur Turhan / Mike Wälte / Thomas Becker / Daniel Kümmel / Christian Schuberth / Rubén Fernández-Busnadiego / Florian Fröhlich / Roland Wedlich-Söldner / Maria Bohnert /
Abstract: Organelle motility enables strategic cellular reorganizations. In yeast, this process depends on the actin cytoskeleton, type V myosin motor proteins, and organelle-specific myosin adaptor proteins. ...Organelle motility enables strategic cellular reorganizations. In yeast, this process depends on the actin cytoskeleton, type V myosin motor proteins, and organelle-specific myosin adaptor proteins. While the myosin adaptors for most organelles are known, the coupling of myosin to lipid droplets (LDs), the cellular lipid storage organelles, remained enigmatic. Using genome-wide screening, we identified Ldm1 (lipid droplet motility 1/Yer085c) as a myosin adaptor. Ldm1 binds to the globular tail domain of the myosin Myo2 and to the LD surface protein Ldo16 to enable actin-dependent LD motility. Ldo16 has additional roles in LD contact sites to the vacuole and the endoplasmic reticulum, suggesting a coordination of LD motility and organelle tethering. Ldm1 has a second role in mitochondrial transport, and elevated Ldm1 levels rescue defects of the mitochondrial Myo2-adaptors Mmr1/Ypt11. Our work identifies the molecular machinery for LD motility and contributes to a comprehensive understanding of acto-myosin-based cellular reorganization.
History
DepositionJul 21, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54489.png

Downloads & links

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Map

FileDownload / File: emd_54489.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
14.6 Å/pix.
x 320 pix.
= 4672. 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-228.072039999999987 - 144.332079999999991
Average (Standard dev.)3.6820273 (±19.818293000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions10241024320
Spacing10241024320
CellA: 14950.4 Å / B: 14950.4 Å / C: 4672.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Tomogram of yeast cell overexpressing Ldm1, treated with alpha-fa...

EntireName: Tomogram of yeast cell overexpressing Ldm1, treated with alpha-factor (unbudded region)
Components
  • Cell: Tomogram of yeast cell overexpressing Ldm1, treated with alpha-factor (unbudded region)

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Supramolecule #1: Tomogram of yeast cell overexpressing Ldm1, treated with alpha-fa...

SupramoleculeName: Tomogram of yeast cell overexpressing Ldm1, treated with alpha-factor (unbudded region)
type: cell / ID: 1 / Parent: 0 / Details: from FIB-milled yeast lamella
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: 7.5
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.05 / Focused ion beam - Duration: 3600 / Focused ion beam - Temperature: 83 K / Focused ion beam - Initial thickness: 5000 / Focused ion beam - Final thickness: 120
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Aquilos 2. 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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 3.29 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 7.0 µm / Calibrated defocus min: 5.0 µm / Calibrated magnification: 33000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 7.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 33000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD (ver. 4.12) / Number images used: 37
CTF correctionType: NONE

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