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- EMDB-57516: Electron tomogram of resin-embedded wild type yeast cells express... -

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Basic information

Entry
Database: EMDB / ID: EMD-57516
TitleElectron tomogram of resin-embedded wild type yeast cells expressing Tcb3(1-490)-chimeraC-GFP
Map dataElectron tomogram of resin-embedded WT yeast cells expressing Tcb3(1-490)-chimeraC-GFP
Sample
  • Cell: Yeast strain WKY0509
Keywordsendoplasmic reticulum / plasma membrane / membrane contact sites / tricalbins / MEMBRANE PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodelectron tomography / cryo EM / negative staining
AuthorsIvanovic L / Boinet AL / Picco A / Zinn E / Ross-Kaschitza D / Kaksonen M / Kukulski W
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: J Cell Sci / Year: 2026
Title: The molecular basis of tricalbin-mediated membrane contact site organization in cells.
Authors: Lazar Ivanović / Anne-Laure Boinet / Andrea Picco / Eliane Zinn / Daniela Ross-Kaschitza / Marko Kaksonen / Wanda Kukulski /
Abstract: Membrane contact sites facilitate molecular exchanges through physical interactions between organelles, connected by specific protein tethers. Among these tethers are the tricalbins, which mediate ...Membrane contact sites facilitate molecular exchanges through physical interactions between organelles, connected by specific protein tethers. Among these tethers are the tricalbins, which mediate contacts between endoplasmic reticulum (ER) and plasma membrane in yeast. Tricalbins are integral to the ER, have a cytosolic lipid-binding domain and bind the plasma membrane through C2 domains. Here, we combine fluorescence recovery after photobleaching with correlative light and 3D electron microscopy to dissect how tricalbins control their localization, dynamic distribution and contact site organization. We find that heteromerization via lipid-binding domains is a prerequisite for tricalbin accumulation at contact sites, membrane curvature sensing and restrained mobility in the ER. By altering tricalbin protein domains, we show that intermembrane distances and intrinsically disordered regions interdependently control distribution and dynamics of contact site tethers. Our study reveals principles of contact site architecture that are fine-tuned by tricalbin domain organization.
History
DepositionApr 18, 2026-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57516.png

Downloads & links

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Map

FileDownload / File: emd_57516.map.gz / Format: CCP4 / Size: 444 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationElectron tomogram of resin-embedded WT yeast cells expressing Tcb3(1-490)-chimeraC-GFP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
11.96 Å/pix.
x 111 pix.
= 1327.56 Å		11.96 Å/pix.
x 2048 pix.
= 24494.08 Å		11.96 Å/pix.
x 2048 pix.
= 24494.08 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: 11.96 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)73.823539999999994 (±10.683335)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-57
Dimensions20482048111
Spacing20482048111
CellA: 24494.08 Å / B: 24494.08 Å / C: 1327.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Yeast strain WKY0509

EntireName: Yeast strain WKY0509
Components
  • Cell: Yeast strain WKY0509

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Supramolecule #1: Yeast strain WKY0509

SupramoleculeName: Yeast strain WKY0509 / type: cell / ID: 1 / Parent: 0 / Details: wild type background, Tcb3(1-490)-chimeraC-GFP
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4
StainingType: NONE / Material: Uranyl acetate
Sugar embeddingMaterial: Lowicryl HM20
VitrificationCryogen name: NITROGEN
High pressure freezingInstrument: OTHER
Details: The value given for _em_high_pressure_freezing.instrument is Leica EMPACT-2. This is not in a list of allowed values {'LEICA EM PACT2', 'EMS-002 RAPID IMMERSION FREEZER', 'LEICA EM PACT', ...Details: The value given for _em_high_pressure_freezing.instrument is Leica EMPACT-2. This is not in a list of allowed values {'LEICA EM PACT2', 'EMS-002 RAPID IMMERSION FREEZER', 'LEICA EM PACT', 'BAL-TEC HPM 010', 'LEICA EM HPM100', 'OTHER'} so OTHER is written into the XML file.
SectioningUltramicrotomy - Instrument: Ultracut E / Ultramicrotomy - Temperature: 293 K / Ultramicrotomy - Final thickness: 200
Fiducial markerManufacturer: Aurion / Diameter: 15 nm

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 999.0 e/Å2
Details: Electron dose unknown. Value specified here is a dummy.
Electron beamAcceleration voltage: 80 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 222
CTF correctionType: NONE

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