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- EMDB-23964: Tomogram of a dividing vegetative cell of Bacillus subtilis (Figu... -

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Basic information

Entry
Database: EMDB / ID: EMD-23964
TitleTomogram of a dividing vegetative cell of Bacillus subtilis (Figure 4A of the manuscript Khanna et al., 2021)
Map dataTomogram of a dividing cell of Bacillus subtilis during vegetative growth (Figure 4A of the manuscript Khanna et al., 2021)
Sample
  • Cell: Dividing vegetative cell of Bacillus subtilis
Biological speciesBacillus subtilis PY79 (bacteria)
Methodelectron tomography / cryo EM
AuthorsKhanna K / Villa E
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM057045 United States
National Science Foundation (NSF, United States)DBI 1920374 United States
CitationJournal: Elife / Year: 2021
Title: Asymmetric localization of the cell division machinery during sporulation.
Authors: Kanika Khanna / Javier Lopez-Garrido / Joseph Sugie / Kit Pogliano / Elizabeth Villa /
Abstract: The Gram-positive bacterium can divide via two modes. During vegetative growth, the division septum is formed at the midcell to produce two equal daughter cells. However, during sporulation, the ...The Gram-positive bacterium can divide via two modes. During vegetative growth, the division septum is formed at the midcell to produce two equal daughter cells. However, during sporulation, the division septum is formed closer to one pole to yield a smaller forespore and a larger mother cell. Using cryo-electron tomography, genetics and fluorescence microscopy, we found that the organization of the division machinery is different in the two septa. While FtsAZ filaments, the major orchestrators of bacterial cell division, are present uniformly around the leading edge of the invaginating vegetative septa, they are only present on the mother cell side of the invaginating sporulation septa. We provide evidence suggesting that the different distribution and number of FtsAZ filaments impact septal thickness, causing vegetative septa to be thicker than sporulation septa already during constriction. Finally, we show that a sporulation-specific protein, SpoIIE, regulates asymmetric divisome localization and septal thickness during sporulation.
History
DepositionMay 11, 2021-
Header (metadata) releaseMay 19, 2021-
Map releaseMay 19, 2021-
UpdateJun 2, 2021-
Current statusJun 2, 2021Processing site: RCSB / Status: Released

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Structure visualization

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

emd_23964.png

Downloads & links

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Map

FileDownload / File: emd_23964.map.gz / Format: CCP4 / Size: 424.8 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationTomogram of a dividing cell of Bacillus subtilis during vegetative growth (Figure 4A of the manuscript Khanna et al., 2021)
Voxel sizeX=Y=Z: 17.06 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)33.627007 (±7.9726343)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-1616250
Dimensions928960500
Spacing960928500
CellA: 16377.6 Å / B: 15831.68 Å / C: 8530.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z17.0617.0617.06
M x/y/z960928500
origin x/y/z0.0000.0000.000
length x/y/z16377.60015831.6808530.000
α/β/γ90.00090.00090.000
start NX/NY/NZ1219875
NX/NY/NZ141223232
MAP C/R/S123
start NC/NR/NS16-16250
NC/NR/NS960928500
D min/max/mean-128.000127.00033.627

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Supplemental data

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Sample components

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Entire : Dividing vegetative cell of Bacillus subtilis

EntireName: Dividing vegetative cell of Bacillus subtilis
Components
  • Cell: Dividing vegetative cell of Bacillus subtilis

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Supramolecule #1: Dividing vegetative cell of Bacillus subtilis

SupramoleculeName: Dividing vegetative cell of Bacillus subtilis / type: cell / ID: 1 / Parent: 0 / Details: Figure 4A of the manuscript Khanna et al., 2021
Source (natural)Organism: Bacillus subtilis PY79 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 5 kV / Focused ion beam - Current: 0.05 nA / Focused ion beam - Duration: 1800 sec. / Focused ion beam - Temperature: 93 K / Focused ion beam - Initial thickness: 1200 nm / Focused ion beam - Final thickness: 200 nm
Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is Thermo Scientific Aquilos. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.0 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

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 48

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