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- EMDB-20337: Cryo-electron tomogram of Bacillus subtilis wild type sporangium ... -

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Basic information

Entry
Database: EMDB / ID: EMD-20337
TitleCryo-electron tomogram of Bacillus subtilis wild type sporangium (engulfing septum) shown in Figure 1H of the publication
Map dataCryo-electron tomogram of wild type Bacillus subtilis sporangium (engulfing septum) shown in Figure 1H of the publication
Sample
  • Cell: Bacillus subtilis wild type sporangium with flat septum
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/Office of the Director1DP2GM123494 United States
National Institutes of Health/National Institute of General Medical SciencesR01-GM057045 United States
CitationJournal: Elife / Year: 2019
Title: The molecular architecture of engulfment during sporulation.
Authors: Kanika Khanna / Javier Lopez-Garrido / Ziyi Zhao / Reika Watanabe / Yuan Yuan / Joseph Sugie / Kit Pogliano / Elizabeth Villa /
Abstract: The study of bacterial cell biology is limited by difficulties in visualizing cellular structures at high spatial resolution within their native milieu. Here, we visualize sporulation using cryo- ...The study of bacterial cell biology is limited by difficulties in visualizing cellular structures at high spatial resolution within their native milieu. Here, we visualize sporulation using cryo-electron tomography coupled with cryo-focused ion beam milling, allowing the reconstruction of native-state cellular sections at molecular resolution. During sporulation, an asymmetrically-positioned septum generates a larger mother cell and a smaller forespore. Subsequently, the mother cell engulfs the forespore. We show that the septal peptidoglycan is not completely degraded at the onset of engulfment. Instead, the septum is uniformly and only slightly thinned as it curves towards the mother cell. Then, the mother cell membrane migrates around the forespore in tiny finger-like projections, whose formation requires the mother cell SpoIIDMP protein complex. We propose that a limited number of SpoIIDMP complexes tether to and degrade the peptidoglycan ahead of the engulfing membrane, generating an irregular membrane front.
History
DepositionJun 21, 2019-
Header (metadata) releaseJul 3, 2019-
Map releaseJul 3, 2019-
UpdateOct 7, 2020-
Current statusOct 7, 2020Processing 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_20337.png

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Map

FileDownload / File: emd_20337.map.gz / Format: CCP4 / Size: 69.7 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationCryo-electron tomogram of wild type Bacillus subtilis sporangium (engulfing septum) shown in Figure 1H of the publication
Voxel sizeX=Y=Z: 19.96 Å
Density
Minimum - Maximum-128 - 127
Average (Standard dev.)28.21398 (±5.434591)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-172-12881
Dimensions644664171
Spacing664644171
CellA: 13253.439 Å / B: 12854.239 Å / C: 3413.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z19.95999849397619.95999844720519.96
M x/y/z664644171
origin x/y/z0.0000.0000.000
length x/y/z13253.43912854.2393413.160
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ162182277
MAP C/R/S123
start NC/NR/NS-128-17281
NC/NR/NS664644171
D min/max/mean-128.000127.00028.214

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Supplemental data

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Sample components

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Entire : Bacillus subtilis wild type sporangium with flat septum

EntireName: Bacillus subtilis wild type sporangium with flat septum
Components
  • Cell: Bacillus subtilis wild type sporangium with flat septum

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Supramolecule #1: Bacillus subtilis wild type sporangium with flat septum

SupramoleculeName: Bacillus subtilis wild type sporangium with flat septum
type: cell / ID: 1 / Parent: 0
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
GridDetails: unspecified
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.03 nA / Focused ion beam - Duration: 3600 sec. / Focused ion beam - Temperature: 100 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 FEI Scios Dual Beam. This is not in a list of allowed values set(['DB235', 'OTHER']) so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 96.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 60

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