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- EMDB-18971: Subtomogram average of YenTc-Chi2-sfGFP from Yersinia entomophaga... -

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Basic information

Entry
Database: EMDB / ID: EMD-18971
TitleSubtomogram average of YenTc-Chi2-sfGFP from Yersinia entomophaga chi2-sfGFP
Map data
Sample
  • Cell: Yersinia entomophaga chi2-sfGFP
KeywordsTc toxin / YenTc / TOXIN
Biological speciesYersinia entomophaga (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 29.6 Å
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 23, 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_18971.png

Downloads & links

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Map

FileDownload / File: emd_18971.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
9.02 Å/pix.
x 80 pix.
= 721.6 Å		9.02 Å/pix.
x 80 pix.
= 721.6 Å		9.02 Å/pix.
x 80 pix.
= 721.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 9.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.75
Minimum - Maximum-7.679821 - 15.63072
Average (Standard dev.)-0.0016716332 (±0.70894974)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 721.60004 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_18971_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18971_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Yersinia entomophaga chi2-sfGFP

EntireName: Yersinia entomophaga chi2-sfGFP
Components
  • Cell: Yersinia entomophaga chi2-sfGFP

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Supramolecule #1: Yersinia entomophaga chi2-sfGFP

SupramoleculeName: Yersinia entomophaga chi2-sfGFP / 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
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.45 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 reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 29.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 412
ExtractionNumber tomograms: 3 / Number images used: 739
Final angle assignmentType: OTHER

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