[English] 日本語
Yorodumi
- EMDB-4966: Subtomogram average of septal junctions from Anabaena sp. PCC7120... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4966
TitleSubtomogram average of septal junctions from Anabaena sp. PCC7120 SjcF1 mutant
Map dataSubtomogram average of septal junctions from Anabaena sp. PCC7120 SjcF1 mutant
Sample
  • Cell: Subtomogram average of septal junctions from Anabaena sp. PCC7120 SjcF1 mutant
Biological speciesNostoc sp. PCC 7120 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 35.0 Å
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 10, 2019-
Header (metadata) releaseJul 24, 2019-
Map releaseJul 24, 2019-
UpdateJul 24, 2019-
Current statusJul 24, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 125
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 125
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4966.png

Downloads & links

-
Map

FileDownload / File: emd_4966.map.gz / Format: CCP4 / Size: 69.3 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of septal junctions from Anabaena sp. PCC7120 SjcF1 mutant
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
13.51 Å/pix.
x 26 pix.
= 351.26 Å		13.51 Å/pix.
x 26 pix.
= 351.26 Å		13.51 Å/pix.
x 26 pix.
= 351.26 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 13.51 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 137.0 / Movie #1: 125
Minimum - Maximum84.154560000000004 - 145.378199999999993
Average (Standard dev.)120.33511 (±5.687446)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions262626
Spacing262626
CellA=B=C: 351.26 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z13.5113.5113.51
M x/y/z262626
origin x/y/z0.0000.0000.000
length x/y/z351.260351.260351.260
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS262626
D min/max/mean84.155145.378120.335

-
Supplemental data

-
Sample components

-
Entire : Subtomogram average of septal junctions from Anabaena sp. PCC7120...

EntireName: Subtomogram average of septal junctions from Anabaena sp. PCC7120 SjcF1 mutant
Components
  • Cell: Subtomogram average of septal junctions from Anabaena sp. PCC7120 SjcF1 mutant

-
Supramolecule #1: Subtomogram average of septal junctions from Anabaena sp. PCC7120...

SupramoleculeName: Subtomogram average of septal junctions from Anabaena sp. PCC7120 SjcF1 mutant
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

-
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 reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: OTHER / Software - Name: PEET / Number subtomograms used: 504
ExtractionNumber tomograms: 14 / Number images used: 116
Final angle assignmentType: OTHER

+
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