[English] 日本語
Yorodumi
- EMDB-10287: CLEM of resin-embedded GFP-Scs2 yeast cell shown in Figure 2A of ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10287
TitleCLEM of resin-embedded GFP-Scs2 yeast cell shown in Figure 2A of publication
Map dataCLEM of resin-embedded GFP-Scs2 yeast cell shown in Figure 2A of publication
Sample
  • Cell: Correlative FM and ET of resin-embedded yeast cell expressing GFP-Scs2
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodelectron tomography / cryo EM / negative staining
AuthorsHoffmann PC / Bharat TAM / Wozny MR / Boulanger J / Miller EA / Kukulski W
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_1201/8 United Kingdom
Wellcome Trust202231/Z/16/Z United Kingdom
Medical Research Council (United Kingdom)MC_UP_1201/10 United Kingdom
CitationJournal: Dev Cell / Year: 2019
Title: Tricalbins Contribute to Cellular Lipid Flux and Form Curved ER-PM Contacts that Are Bridged by Rod-Shaped Structures.
Authors: Patrick C Hoffmann / Tanmay A M Bharat / Michael R Wozny / Jerome Boulanger / Elizabeth A Miller / Wanda Kukulski /
Abstract: Lipid flow between cellular organelles occurs via membrane contact sites. Extended-synaptotagmins, known as tricalbins in yeast, mediate lipid transfer between the endoplasmic reticulum (ER) and ...Lipid flow between cellular organelles occurs via membrane contact sites. Extended-synaptotagmins, known as tricalbins in yeast, mediate lipid transfer between the endoplasmic reticulum (ER) and plasma membrane (PM). How these proteins regulate membrane architecture to transport lipids across the aqueous space between bilayers remains unknown. Using correlative microscopy, electron cryo-tomography, and high-throughput genetics, we address the interplay of architecture and function in budding yeast. We find that ER-PM contacts differ in protein composition and membrane morphology, not in intermembrane distance. In situ electron cryo-tomography reveals the molecular organization of tricalbin-mediated contacts, suggesting a structural framework for putative lipid transfer. Genetic analysis uncovers functional overlap with cellular lipid routes, such as maintenance of PM asymmetry. Further redundancies are suggested for individual tricalbin protein domains. We propose a modularity of molecular and structural functions of tricalbins and of their roles within the cellular network of lipid distribution pathways.
History
DepositionSep 4, 2019-
Header (metadata) releaseNov 13, 2019-
Map releaseNov 13, 2019-
UpdateDec 4, 2019-
Current statusDec 4, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Supplemental images

emd_10287.png

Downloads & links

-
Map

FileDownload / File: emd_10287.map.gz / Format: CCP4 / Size: 768 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationCLEM of resin-embedded GFP-Scs2 yeast cell shown in Figure 2A of publication
Voxel sizeX=Y=Z: 11.02 Å
Density
Minimum - Maximum-128 - 127
Average (Standard dev.)6.119652 (±8.728586)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-96
Dimensions20482048192
Spacing20482048192
CellA: 22568.96 Å / B: 22568.96 Å / C: 2115.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z11.02000048828111.02000048828111.02
M x/y/z20482048192
origin x/y/z0.0000.0000.000
length x/y/z22568.96122568.9612115.840
α/β/γ90.00090.00090.000
start NX/NY/NZ111-94150
NX/NY/NZ111123111
MAP C/R/S123
start NC/NR/NS00-96
NC/NR/NS20482048192
D min/max/mean-128.000127.0006.120

-
Supplemental data

-
Sample components

-
Entire : Correlative FM and ET of resin-embedded yeast cell expressing GFP-Scs2

EntireName: Correlative FM and ET of resin-embedded yeast cell expressing GFP-Scs2
Components
  • Cell: Correlative FM and ET of resin-embedded yeast cell expressing GFP-Scs2

-
Supramolecule #1: Correlative FM and ET of resin-embedded yeast cell expressing GFP-Scs2

SupramoleculeName: Correlative FM and ET of resin-embedded yeast cell expressing GFP-Scs2
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.4
StainingType: NONE / Material: Uranyl Acetate
Details: 0.03-0.05 % uranyl acetate during freeze substitution and post-staining of sections with Reynold's lead citrate
Sugar embeddingMaterial: Lowicryl HM20
VitrificationCryogen name: NITROGEN
High pressure freezingInstrument: OTHER
Details: The value given for _emd_high_pressure_freezing.instrument is Leica EM HPM100. This is not in a list of allowed values set(['LEICA EM PACT2', 'LEICA EM PACT', 'EMS-002 RAPID IMMERSION ...Details: The value given for _emd_high_pressure_freezing.instrument is Leica EM HPM100. This is not in a list of allowed values set(['LEICA EM PACT2', 'LEICA EM PACT', 'EMS-002 RAPID IMMERSION FREEZER', 'OTHER', 'LEICA EM HPM100', 'BAL-TEC HPM 010']) so OTHER is written into the XML file.
SectioningUltramicrotomy - Instrument: Reichert Ultracut E / Ultramicrotomy - Temperature: 298 K / Ultramicrotomy - Final thickness: 270 nm
Fiducial marker
ManufacturerDiameter
Electron Microscopy Sciences15 nm
Life Technologies50 nm

-
Electron microscopy

MicroscopeFEI TECNAI F20
DetailsSTEM mode on an axial brightfield detector with a high-tilt tomography holder (Fischione Instruments, Model 2020)
Image recordingFilm or detector model: OTHER / Average electron dose: 1000.0 e/Å2
Details: ET was done in STEM mode on an axial brightfield detector with a high-tilt tomography holder at 1.102 nm pixel size with a camera length of 200 mm. [NOTE: Electron dose unknown. Value specified here is a dummy]
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: eTomo / Details: 223 tilted images used from two axes / Number images used: 223
CTF correctionSoftware - Name: eTomo

+
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