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- EMDB-57523: Cryo-electron tomogram of yeast cells expressing Tcb3(191-490)-ch... -

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Basic information

Entry
Database: EMDB / ID: EMD-57523
TitleCryo-electron tomogram of yeast cells expressing Tcb3(191-490)-chimeraC-GFP, deleted for tcb1/2, scs2/22 and ist2.
Map dataCryo-electron tomogram of 5delta yeast cells expressing Tcb3(191-490)-chimeraC-GFP
Sample
  • Cell: Yeast strain WKY0530
Keywordsendoplasmic reticulum / plasma membrane / membrane contact sites / tricalbins / MEMBRANE PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodelectron tomography / cryo EM
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_57523.png

Downloads & links

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Map

FileDownload / File: emd_57523.map.gz / Format: CCP4 / Size: 392 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationCryo-electron tomogram of 5delta yeast cells expressing Tcb3(191-490)-chimeraC-GFP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
11.63 Å/pix.
x 196 pix.
= 2279.48 Å		11.63 Å/pix.
x 1024 pix.
= 11909.12 Å		11.63 Å/pix.
x 1024 pix.
= 11909.12 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: 11.63 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-10859.0 - 4935.0
Average (Standard dev.)55.907670000000003 (±723.07770000000005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-99
Dimensions10241024196
Spacing10241024196
CellA: 11909.12 Å / B: 11909.12 Å / C: 2279.48 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 WKY0530

EntireName: Yeast strain WKY0530
Components
  • Cell: Yeast strain WKY0530

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Supramolecule #1: Yeast strain WKY0530

SupramoleculeName: Yeast strain WKY0530 / type: cell / ID: 1 / Parent: 0
Details: scs2delta, scs22delta, tcb1delta, tcb2delta, ist2delta, Tcb3(191-490)-chimeraC-GFP
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: 7.4
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 1 / Focused ion beam - Duration: 2000 / Focused ion beam - Temperature: 80 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is TFS Aquilos 2. 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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 1.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD
Details: The deposited reconstruction is 2x binned compared to the original acquisition.
Number images used: 113
CTF correctionType: NONE

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