[English] 日本語
Yorodumi
- EMDB-19405: Tomograms of spoIVB Bacillus subtilis sporangia -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-19405
TitleTomograms of spoIVB Bacillus subtilis sporangia
Map data
Sample
  • Cell: Sporulating cells of Bacillus subtilis strain 168 deleted from the spoIVB gene
KeywordsSporulation / Bacillus subtilis / coat / macromolecular assemblies / STRUCTURAL PROTEIN
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
Methodelectron tomography / cryo EM
AuthorsBauda E / Gallet B / Moravcova J / Effantin G / Chan H / Novacek J / Jouneau PH / Rodrigues CDA / Schoehn G / Moriscot C / Morlot C
Funding support France, European Union, Australia, 10 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-10-INBS-0005-02 France
Agence Nationale de la Recherche (ANR)ANR-17-EURE-0003 France
Grenoble Alliance for Integrated Structural Cell Biology (GRAL) France
Grenoble Instruct-ERIC Center (ISBG) France
Grenoble Instruct-ERIC Center (ISBG) France
Grenoble Instruct-ERIC Center (ISBG)PID1697 France
Grenoble Instruct-ERIC Center (ISBG)PID17035 France
European Regional Development FundUP CIISBEuropean Union
iNEXT-Discovery871037European Union
Australian Research Council (ARC)DP190100793 Australia
CitationJournal: Nat Commun / Year: 2024
Title: Ultrastructure of macromolecular assemblies contributing to bacterial spore resistance revealed by in situ cryo-electron tomography.
Authors: Elda Bauda / Benoit Gallet / Jana Moravcova / Gregory Effantin / Helena Chan / Jiri Novacek / Pierre-Henri Jouneau / Christopher D A Rodrigues / Guy Schoehn / Christine Moriscot / Cecile Morlot /
Abstract: Bacterial spores owe their incredible resistance capacities to molecular structures that protect the cell content from external aggressions. Among the determinants of resistance are the quaternary ...Bacterial spores owe their incredible resistance capacities to molecular structures that protect the cell content from external aggressions. Among the determinants of resistance are the quaternary structure of the chromosome and an extracellular shell made of proteinaceous layers (the coat), the assembly of which remains poorly understood. Here, in situ cryo-electron tomography on lamellae generated by cryo-focused ion beam micromachining provides insights into the ultrastructural organization of Bacillus subtilis sporangia. The reconstructed tomograms reveal that early during sporulation, the chromosome in the forespore adopts a toroidal structure harboring 5.5-nm thick fibers. At the same stage, coat proteins at the surface of the forespore form a stack of amorphous or structured layers with distinct electron density, dimensions and organization. By analyzing mutant strains using cryo-electron tomography and transmission electron microscopy on resin sections, we distinguish seven nascent coat regions with different molecular properties, and propose a model for the contribution of coat morphogenetic proteins.
History
DepositionJan 12, 2024-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_19405.png

Downloads & links

-
Map

FileDownload / File: emd_19405.map.gz / Format: CCP4 / Size: 3.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 8.812 Å
Density
Minimum - Maximum-1.3624908 - 2.3029158
Average (Standard dev.)0.000021582664 (±0.09383478)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-246-1-1
Dimensions25019201856
Spacing19202501856
CellA: 16919.041 Å / B: 2203.0 Å / C: 16355.072 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #6

Fileemd_19405_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #5

Fileemd_19405_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #4

Fileemd_19405_additional_3.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #3

Fileemd_19405_additional_4.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #2

Fileemd_19405_additional_5.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_19405_additional_6.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Sporulating cells of Bacillus subtilis strain 168 deleted from th...

EntireName: Sporulating cells of Bacillus subtilis strain 168 deleted from the spoIVB gene
Components
  • Cell: Sporulating cells of Bacillus subtilis strain 168 deleted from the spoIVB gene

-
Supramolecule #1: Sporulating cells of Bacillus subtilis strain 168 deleted from th...

SupramoleculeName: Sporulating cells of Bacillus subtilis strain 168 deleted from the spoIVB gene
type: cell / ID: 1 / Parent: 0
Details: View of a developing spore within a Bacillus subtilis mother cell
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
Cryo protectant5% glycerol
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 1 / Focused ion beam - Duration: 20 / Focused ion beam - Temperature: 83 K / Focused ion beam - Initial thickness: 4000 / Focused ion beam - Final thickness: 150
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Versa 3D Dual Beam. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

-
Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 20.0 µm / Nominal defocus min: 10.0 µm / Nominal magnification: 33000
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 85.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Number images used: 41

+
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