[English] 日本語
Yorodumi
- EMDB-4305: Correlative cryo-FM and Cryo-ET of vitreous sections of yeast cells -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4305
TitleCorrelative cryo-FM and Cryo-ET of vitreous sections of yeast cells
Map dataThis is a tomogram of a vitreous section of yeast cells expressing Pil1-GFP. There are two eisosomal sites seen.
Sample
  • Cell: Saccharomyces cerevisiae
Biological speciesSaccharomyces cerevisiae S288c (yeast)
Methodelectron tomography
AuthorsBharat TAM / Hoffmann PC / Kukulski W
CitationJournal: Structure / Year: 2018
Title: Correlative Microscopy of Vitreous Sections Provides Insights into BAR-Domain Organization In Situ.
Authors: Tanmay A M Bharat / Patrick C Hoffmann / Wanda Kukulski /
Abstract: Electron microscopy imaging of macromolecular complexes in their native cellular context is limited by the inherent difficulty to acquire high-resolution tomographic data from thick cells and to ...Electron microscopy imaging of macromolecular complexes in their native cellular context is limited by the inherent difficulty to acquire high-resolution tomographic data from thick cells and to specifically identify elusive structures within crowded cellular environments. Here, we combined cryo-fluorescence microscopy with electron cryo-tomography of vitreous sections into a coherent correlative microscopy workflow, ideal for detection and structural analysis of elusive protein assemblies in situ. We used this workflow to address an open question on BAR-domain coating of yeast plasma membrane compartments known as eisosomes. BAR domains can sense or induce membrane curvature, and form scaffold-like membrane coats in vitro. Our results demonstrate that in cells, the BAR protein Pil1 localizes to eisosomes of varying membrane curvature. Sub-tomogram analysis revealed a dense protein coat on curved eisosomes, which was not present on shallow eisosomes, indicating that while BAR domains can assemble at shallow membranes in vivo, scaffold formation is tightly coupled to curvature generation.
History
DepositionFeb 21, 2018-
Header (metadata) releaseMay 2, 2018-
Map releaseMay 2, 2018-
UpdateJun 13, 2018-
Current statusJun 13, 2018Processing 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_4305.png

Downloads & links

-
Map

FileDownload / File: emd_4305.map.gz / Format: CCP4 / Size: 221.7 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationThis is a tomogram of a vitreous section of yeast cells expressing Pil1-GFP. There are two eisosomal sites seen.
Voxel sizeX=Y=Z: 14.34 Å
Density
Minimum - Maximum-128. - 127.
Average (Standard dev.)64.033810000000003 (±97.644189999999995)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-1616151
Dimensions926958262
Spacing958926262
CellA: 13737.72 Å / B: 13278.84 Å / C: 3757.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z14.3414.3414.34
M x/y/z958926262
origin x/y/z0.0000.0000.000
length x/y/z13737.72013278.8403757.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS16-16151
NC/NR/NS958926262
D min/max/mean-128.000127.00064.034

-
Supplemental data

-
Sample components

-
Entire : Saccharomyces cerevisiae

EntireName: Saccharomyces cerevisiae (brewer's yeast)
Components
  • Cell: Saccharomyces cerevisiae

-
Supramolecule #1: Saccharomyces cerevisiae

SupramoleculeName: Saccharomyces cerevisiae / type: cell / ID: 1 / Parent: 0
Details: genotype: MATalpha, his3delta200, leu2-3,112, ura3-52, lys2-801, PIL1-EGFP::HIS3MX6
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)

-
Experimental details

-
Structure determination

Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.4
High pressure freezingInstrument: OTHER
Details: The value given for _emd_high_pressure_freezing.instrument is Leica HPM100. This is not in a list of allowed values set(['LEICA EM PACT2', 'LEICA EM PACT', 'EMS-002 RAPID IMMERSION FREEZER', ...Details: The value given for _emd_high_pressure_freezing.instrument is Leica 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: Leica / Ultramicrotomy - Temperature: 100 K / Ultramicrotomy - Final thickness: 150
Fiducial markerManufacturer: CMC Utrecht / Diameter: 10 nm

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 0.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: IMOD / Number images used: 121
CTF correctionSoftware - Name: IMOD

+
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://pdbjlvh1.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