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- EMDB-18958: Cryo-electron tomogram of Yersinia entomophaga MH96 cells -

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Basic information

Entry
Database: EMDB / ID: EMD-18958
TitleCryo-electron tomogram of Yersinia entomophaga MH96 cells
Map data
Sample
  • Cell: Yersinia entomophaga MH96
KeywordsTc toxin / YenTc / TOXIN
Biological speciesYersinia entomophaga (bacteria)
Methodelectron tomography / cryo EM
AuthorsFeldmueller M / Pilhofer M
Funding supportEuropean Union, Switzerland, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)679209European Union
Swiss National Science Foundation310030_212592 Switzerland
CitationJournal: Nat Microbiol / Year: 2024
Title: Stepwise assembly and release of Tc toxins from Yersinia entomophaga.
Authors: Miki Feldmüller / Charles F Ericson / Pavel Afanasyev / Yun-Wei Lien / Gregor L Weiss / Florian Wollweber / Marion Schoof / Mark Hurst / Martin Pilhofer /
Abstract: Tc toxins are virulence factors of bacterial pathogens. Although their structure and intoxication mechanism are well understood, it remains elusive where this large macromolecular complex is ...Tc toxins are virulence factors of bacterial pathogens. Although their structure and intoxication mechanism are well understood, it remains elusive where this large macromolecular complex is assembled and how it is released. Here we show by an integrative multiscale imaging approach that Yersinia entomophaga Tc (YenTc) toxin components are expressed only in a subpopulation of cells that are 'primed' with several other potential virulence factors, including filaments of the protease M66/StcE. A phage-like lysis cassette is required for YenTc release; however, before resulting in complete cell lysis, the lysis cassette generates intermediate 'ghost' cells, which may serve as assembly compartments and become packed with assembled YenTc holotoxins. We hypothesize that this stepwise mechanism evolved to minimize the number of cells that need to be killed. The occurrence of similar lysis cassettes in diverse organisms indicates a conserved mechanism for Tc toxin release that may apply to other extracellular macromolecular machines.
History
DepositionNov 22, 2023-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18958.png

Downloads & links

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Map

FileDownload / File: emd_18958.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
18.04 Å/pix.
x 450 pix.
= 8118. Å		18.04 Å/pix.
x 1440 pix.
= 25977.602 Å		18.04 Å/pix.
x 1024 pix.
= 18472.961 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 18.04 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-13.0 - 13.0
Average (Standard dev.)0.15587768 (±1.1233953)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-208208-225
Dimensions14401024450
Spacing10241440450
CellA: 18472.96 Å / B: 25977.602 Å / C: 8118.0005 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Yersinia entomophaga MH96

EntireName: Yersinia entomophaga MH96
Components
  • Cell: Yersinia entomophaga MH96

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Supramolecule #1: Yersinia entomophaga MH96

SupramoleculeName: Yersinia entomophaga MH96 / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Yersinia entomophaga (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: 7.5
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.05 / Focused ion beam - Duration: 1740 / Focused ion beam - Temperature: 123 K / Focused ion beam - Initial thickness: 2000 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Zeiss Crossbeam 550. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.46 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 8.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 61

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