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- EMDB-15355: Electron cryo-tomography of the ER-mitochondria encounter structu... -

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Entry
Database: EMDB / ID: EMD-15355
TitleElectron cryo-tomography of the ER-mitochondria encounter structure ERMES
Map dataElectron cryo-tomogram of cryo-FIB-milled yeast cell, acquired at position of Mdm34-mNeonGreen signal.
Sample
  • Cell: Budding yeast expressing Mdm34-mNeonGreen
Keywordscryo-ET / cryo-FIB milling / cryo-CLEM / membrane contact sites / ERMES / lipid transfer protein / LIPID TRANSPORT
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodelectron tomography / cryo EM
AuthorsWozny MR / Di Luca A / Morado DR / Picco A / Khaddaj R / Campomanes P / Ivanovic L / Hoffmann PC / Miller EA / Vanni S / Kukulski W
Funding support United Kingdom, Canada, Switzerland, European Union, 7 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MC_UP_1201/08 United Kingdom
UK Research and Innovation (UKRI)MC_UP_1201/10 United Kingdom
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Swiss National Science Foundation185544 Switzerland
Swiss National Science Foundation201158 Switzerland
Swiss National Science Foundation194807 Switzerland
European Research Council (ERC)803952European Union
CitationJournal: Nature / Year: 2023
Title: In situ architecture of the ER-mitochondria encounter structure.
Authors: Michael R Wozny / Andrea Di Luca / Dustin R Morado / Andrea Picco / Rasha Khaddaj / Pablo Campomanes / Lazar Ivanović / Patrick C Hoffmann / Elizabeth A Miller / Stefano Vanni / Wanda Kukulski /
Abstract: The endoplasmic reticulum and mitochondria are main hubs of eukaryotic membrane biogenesis that rely on lipid exchange via membrane contact sites, but the underpinning mechanisms remain poorly ...The endoplasmic reticulum and mitochondria are main hubs of eukaryotic membrane biogenesis that rely on lipid exchange via membrane contact sites, but the underpinning mechanisms remain poorly understood. In yeast, tethering and lipid transfer between the two organelles is mediated by the endoplasmic reticulum-mitochondria encounter structure (ERMES), a four-subunit complex of unresolved stoichiometry and architecture. Here we determined the molecular organization of ERMES within Saccharomyces cerevisiae cells using integrative structural biology by combining quantitative live imaging, cryo-correlative microscopy, subtomogram averaging and molecular modelling. We found that ERMES assembles into approximately 25 discrete bridge-like complexes distributed irregularly across a contact site. Each bridge consists of three synaptotagmin-like mitochondrial lipid binding protein domains oriented in a zig-zag arrangement. Our molecular model of ERMES reveals a pathway for lipids. These findings resolve the in situ supramolecular architecture of a major inter-organelle lipid transfer machinery and provide a basis for the mechanistic understanding of lipid fluxes in eukaryotic cells.
History
DepositionJul 7, 2022-
Header (metadata) releaseMar 22, 2023-
Map releaseMar 22, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_15355.map.gz / Format: CCP4 / Size: 1 GB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationElectron cryo-tomogram of cryo-FIB-milled yeast cell, acquired at position of Mdm34-mNeonGreen signal.
Voxel sizeX=Y=Z: 10.74 Å
Density
Minimum - Maximum-68.0 - 45.0
Average (Standard dev.)0.5220342 (±5.3679357)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-208208-375
Dimensions14401023750
Spacing10231440750
CellA: 10987.02 Å / B: 15465.6 Å / C: 8055.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Budding yeast expressing Mdm34-mNeonGreen

EntireName: Budding yeast expressing Mdm34-mNeonGreen
Components
  • Cell: Budding yeast expressing Mdm34-mNeonGreen

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Supramolecule #1: Budding yeast expressing Mdm34-mNeonGreen

SupramoleculeName: Budding yeast expressing Mdm34-mNeonGreen / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae S288C (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
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: 1800 / Focused ion beam - Temperature: 100 K / Focused ion beam - Initial thickness: 5000 / Focused ion beam - Final thickness: 320
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is FEI Scios. 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 121

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