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- EMDB-18970: Subtomogram average of M66 filaments in Yersinia entomophaga cells -

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Basic information

Entry
Database: EMDB / ID: EMD-18970
TitleSubtomogram average of M66 filaments in Yersinia entomophaga cells
Map data
Sample
  • Cell: Yersinia entomophaga delta LC
KeywordsTc toxin / YenTc / TOXIN
Biological speciesYersinia entomophaga (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 9.89 Å
AuthorsFeldmueller M / Afanasyev P / 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_18970.png

Downloads & links

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Map

FileDownload / File: emd_18970.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 2.678 Å
Density
Contour LevelBy AUTHOR: 0.75
Minimum - Maximum-1.5394512 - 2.3801248
Average (Standard dev.)0.01074355 (±0.17524609)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 514.176 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18970_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18970_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18970_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 delta LC

EntireName: Yersinia entomophaga delta LC
Components
  • Cell: Yersinia entomophaga delta LC

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Supramolecule #1: Yersinia entomophaga delta LC

SupramoleculeName: Yersinia entomophaga delta LC / 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

MicroscopeFEI TITAN
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 19500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.45 e/Å2

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Image processing

ExtractionNumber tomograms: 42 / Number images used: 35332 / Software: (Name: Dynamo, RELION)
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 23158
FSC plot (resolution estimation)

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