[English] 日本語
Yorodumi
- EMDB-4954: Electron cryotomogram of septal region from FIB milled Anabaena s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4954
TitleElectron cryotomogram of septal region from FIB milled Anabaena sp. PCC7120 FraC/FraD mutant filament
Map dataElectron cryotomogram of septal region from FIB milled Anabaena sp. PCC7120 FraC/FraD mutant filament
Sample
  • Cell: Electron cryotomogram of septal region from FIB milled Anabaena sp. PCC7120 FraC/FraD mutant filament
Biological speciesNostoc sp. PCC 7120 (bacteria)
Methodelectron tomography / cryo EM
AuthorsWeiss GL / Kieninger A / Maldener I / Forchhammer K / Pilhofer M
Funding support Germany, Switzerland, 3 items
OrganizationGrant numberCountry
German Research FoundationSFB766 Germany
European Research Council#679209 Switzerland
Swiss National Science Foundation#31003A_179255 Switzerland
CitationJournal: Cell / Year: 2019
Title: Structure and Function of a Bacterial Gap Junction Analog.
Authors: Gregor L Weiss / Ann-Katrin Kieninger / Iris Maldener / Karl Forchhammer / Martin Pilhofer /
Abstract: Multicellular lifestyle requires cell-cell connections. In multicellular cyanobacteria, septal junctions enable molecular exchange between sister cells and are required for cellular differentiation. ...Multicellular lifestyle requires cell-cell connections. In multicellular cyanobacteria, septal junctions enable molecular exchange between sister cells and are required for cellular differentiation. The structure of septal junctions is poorly understood, and it is unknown whether they are capable of controlling intercellular communication. Here, we resolved the in situ architecture of septal junctions by electron cryotomography of cryo-focused ion beam-milled cyanobacterial filaments. Septal junctions consisted of a tube traversing the septal peptidoglycan. Each tube end comprised a FraD-containing plug, which was covered by a cytoplasmic cap. Fluorescence recovery after photobleaching showed that intercellular communication was blocked upon stress. Gating was accompanied by a reversible conformational change of the septal junction cap. We provide the mechanistic framework for a cell junction that predates eukaryotic gap junctions by a billion years. The conservation of a gated dynamic mechanism across different domains of life emphasizes the importance of controlling molecular exchange in multicellular organisms.
History
DepositionMay 9, 2019-
Header (metadata) releaseJul 24, 2019-
Map releaseJul 24, 2019-
UpdateJul 24, 2019-
Current statusJul 24, 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_4954.png

Downloads & links

-
Map

FileDownload / File: emd_4954.map.gz / Format: CCP4 / Size: 367.9 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationElectron cryotomogram of septal region from FIB milled Anabaena sp. PCC7120 FraC/FraD mutant filament
Voxel sizeX=Y=Z: 13.51 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)-5.048199 (±26.729671)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-1616217
Dimensions928960433
Spacing960928433
CellA: 12969.601 Å / B: 12537.28 Å / C: 5849.83 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z13.51000104166713.5113.51
M x/y/z960928433
origin x/y/z0.0000.0000.000
length x/y/z12969.60112537.2805849.830
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS16-16217
NC/NR/NS960928433
D min/max/mean-128.000127.000-5.048

-
Supplemental data

-
Sample components

-
Entire : Electron cryotomogram of septal region from FIB milled Anabaena s...

EntireName: Electron cryotomogram of septal region from FIB milled Anabaena sp. PCC7120 FraC/FraD mutant filament
Components
  • Cell: Electron cryotomogram of septal region from FIB milled Anabaena sp. PCC7120 FraC/FraD mutant filament

-
Supramolecule #1: Electron cryotomogram of septal region from FIB milled Anabaena s...

SupramoleculeName: Electron cryotomogram of septal region from FIB milled Anabaena sp. PCC7120 FraC/FraD mutant filament
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 18 nA / Focused ion beam - Duration: 1 sec. / Focused ion beam - Temperature: 128 K / Focused ion beam - Initial thickness: 3000 nm / Focused ion beam - Final thickness: 200 nm
Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Helios NanoLab 600i. This is not in a list of allowed values set(['DB235', 'OTHER']) so OTHER is ...Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Helios NanoLab 600i. This is not in a list of allowed values set(['DB235', 'OTHER']) so OTHER is written into the XML file.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 2.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionNumber images used: 61

+
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