[English] 日本語
Yorodumi
- EMDB-16871: Subtomogram average of short bridges of the yeast ER-mitochondria... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16871
TitleSubtomogram average of short bridges of the yeast ER-mitochondria encounter structure (ERMES). The population half containing shorter bridge structures was averaged.
Map dataSubtomogram average (STA) map of short ERMES bridge structures. The data set of all bridges was split into halves according to bridge length. The map has been aligned to the STA map of all bridges.
Sample
  • Cell: Budding yeast cells expressing Mdm34-mNeonGreen, a component of the ER-mitochondria encounter structure (ERMES).
KeywordsERMES / lipid transfer protein / membrane contact sites / SMP domains / LIPID TRANSPORT
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 29.0 Å
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
Medical Research Council (MRC, United Kingdom)MC_UP_1201/8 United Kingdom
Medical Research Council (MRC, United Kingdom)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
DepositionMar 19, 2023-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateJun 7, 2023-
Current statusJun 7, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16871.png

Downloads & links

-
Map

FileDownload / File: emd_16871.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average (STA) map of short ERMES bridge structures. The data set of all bridges was split into halves according to bridge length. The map has been aligned to the STA map of all bridges.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.37 Å/pix.
x 120 pix.
= 644.16 Å		5.37 Å/pix.
x 120 pix.
= 644.16 Å		5.37 Å/pix.
x 120 pix.
= 644.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.368 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.60045236 - 1.0418863
Average (Standard dev.)0.0002155369 (±0.08242928)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 644.16003 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Half map b, masked. Together with masked half...

Fileemd_16871_additional_1.map
AnnotationHalf map b, masked. Together with masked half map a, this was used for resolution estimate.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Half map a, masked. Together with masked half...

Fileemd_16871_additional_2.map
AnnotationHalf map a, masked. Together with masked half map b, this was used for resolution estimate.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: This is the main STA map of short...

Fileemd_16871_additional_3.map
AnnotationThis is the main STA map of short bridges, not aligned to the STA map of all bridges.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map a, unmasked

Fileemd_16871_half_map_1.map
AnnotationHalf map a, unmasked
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map b, unmasked

Fileemd_16871_half_map_2.map
AnnotationHalf map b, unmasked
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Budding yeast cells expressing Mdm34-mNeonGreen, a component of t...

EntireName: Budding yeast cells expressing Mdm34-mNeonGreen, a component of the ER-mitochondria encounter structure (ERMES).
Components
  • Cell: Budding yeast cells expressing Mdm34-mNeonGreen, a component of the ER-mitochondria encounter structure (ERMES).

-
Supramolecule #1: Budding yeast cells expressing Mdm34-mNeonGreen, a component of t...

SupramoleculeName: Budding yeast cells expressing Mdm34-mNeonGreen, a component of the ER-mitochondria encounter structure (ERMES).
type: cell / ID: 1 / Parent: 0
Details: Yeast cells were cryo-FIB-milled, imaged by cryo-fluorescence microscopy and electron cryo-tomograms were acquired at localisations of Mdm34-mNeonGreen fluorescent signals.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: S288C

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 6
Details: Synthetic complete medium without tryptophan, with 2% glucose and 15% dextran
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
DetailsPlunge-frozen grids with yeast cells were subjected to cryo-FIB milling followed by cryo-fluorescence microscopy prior to cryo-ET.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 29.0 Å / Resolution method: FSC 0.143 CUT-OFF
Details: This STA map was obtained using half of the subtomograms that were used to obtain the map of all ERMES bridges (1098 subtomograms). The data set was split according to bridge length; here ...Details: This STA map was obtained using half of the subtomograms that were used to obtain the map of all ERMES bridges (1098 subtomograms). The data set was split according to bridge length; here the half containing shorter bridges was used.
Number subtomograms used: 549
ExtractionNumber tomograms: 51 / Number images used: 1133
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more