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- EMDB-16618: Structure of Yersinia entomophaga Tc toxin from FIB-milled sphero... -

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Basic information

Entry
Database: EMDB / ID: EMD-16618
TitleStructure of Yersinia entomophaga Tc toxin from FIB-milled spheroplasts
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)
Methodsubtomogram averaging / cryo EM / Resolution: 27.0 Å
AuthorsSitsel O / Wang Z / Janning P / Kroczek L / Wagner T / 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
DepositionFeb 3, 2023-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16618.png

Downloads & links

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Map

FileDownload / File: emd_16618.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.94 Å/pix.
x 128 pix.
= 760.32 Å		5.94 Å/pix.
x 128 pix.
= 760.32 Å		5.94 Å/pix.
x 128 pix.
= 760.32 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 5.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.158
Minimum - Maximum-0.34924614 - 0.73421615
Average (Standard dev.)0.00079582055 (±0.032516673)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 760.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16618_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_16618_half_map_1.map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_16618_half_map_2.map
Projections & Slices
AxesZYX

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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
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4 / Component - Concentration: 1.0 x / Component - Formula: PBS / Component - Name: Phosphate-Buffered Saline
VitrificationCryogen name: ETHANE

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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: 3.85 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 7 / Number images used: 528
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.5)
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 27.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 528
FSC plot (resolution estimation)

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