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- EMDB-15406: Tomogram of Yersinia entomophaga in the post-endolysin state -

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Basic information

Entry
Database: EMDB / ID: EMD-15406
TitleTomogram of Yersinia entomophaga in the post-endolysin state
Map data
Sample
  • Cell: Yersinia entomophaga strain Ara-YenR (YeIspn/YeOspn KO)
KeywordsVirulence / Secretion / Tc toxin / Type 10 secretion system / TOXIN
Biological speciesYersinia entomophaga (bacteria)
Methodelectron tomography / cryo EM
AuthorsSitsel O / Wang Z / Janning P / Kroczek L / Raunser S
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Microbiol / Year: 2024
Title: Yersinia entomophaga Tc toxin is released by T10SS-dependent lysis of specialized cell subpopulations.
Authors: Oleg Sitsel / Zhexin Wang / Petra Janning / Lara Kroczek / Thorsten Wagner / Stefan Raunser /
Abstract: Disease-causing bacteria secrete numerous toxins to invade and subjugate their hosts. Unlike many smaller toxins, the secretion machinery of most large toxins remains enigmatic. By combining genomic ...Disease-causing bacteria secrete numerous toxins to invade and subjugate their hosts. Unlike many smaller toxins, the secretion machinery of most large toxins remains enigmatic. By combining genomic editing, proteomic profiling and cryo-electron tomography of the insect pathogen Yersinia entomophaga, we demonstrate that a specialized subset of these cells produces a complex toxin cocktail, including the nearly ribosome-sized Tc toxin YenTc, which is subsequently exported by controlled cell lysis using a transcriptionally coupled, pH-dependent type 10 secretion system (T10SS). Our results dissect the Tc toxin export process by a T10SS, identifying that T10SSs operate via a previously unknown lytic mode of action and establishing them as crucial players in the size-insensitive release of cytoplasmically folded toxins. With T10SSs directly embedded in Tc toxin operons of major pathogens, we anticipate that our findings may model an important aspect of pathogenesis in bacteria with substantial impact on agriculture and healthcare.
History
DepositionJul 18, 2022-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15406.png

Downloads & links

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Map

FileDownload / File: emd_15406.map.gz / Format: CCP4 / Size: 210.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
11.87 Å/pix.
x 150 pix.
= 1780.8 Å		11.87 Å/pix.
x 720 pix.
= 8547.84 Å		11.87 Å/pix.
x 512 pix.
= 6078.464 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: 11.872 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-3.4085522 - 1.9436831
Average (Standard dev.)-0.0009622595 (±0.043052882)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-75
Dimensions720512150
Spacing512720150
CellA: 6078.464 Å / B: 8547.84 Å / C: 1780.7999 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 strain Ara-YenR (YeIspn/YeOspn KO)

EntireName: Yersinia entomophaga strain Ara-YenR (YeIspn/YeOspn KO)
Components
  • Cell: Yersinia entomophaga strain Ara-YenR (YeIspn/YeOspn KO)

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Supramolecule #1: Yersinia entomophaga strain Ara-YenR (YeIspn/YeOspn KO)

SupramoleculeName: Yersinia entomophaga strain Ara-YenR (YeIspn/YeOspn KO)
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Yersinia entomophaga (bacteria) / Strain: Ara-YenR (YeIspn/YeOspn KO)

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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: 7.4 / Component - Concentration: 1.0 x / Component - Formula: PBS / Component - Name: Phosphate-Buffered Saline
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE
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: 60 / Focused ion beam - Temperature: 90 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 100
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is FEI Aquilos. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.
Fiducial markerManufacturer: Aurion / Diameter: 5 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 8.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 64000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
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: 130.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 37

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