+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15405 | |||||||||
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Title | Tomogram of Yersinia entomophaga in the post-holin state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Virulence / Secretion / Tc toxin / Type 10 secretion system / TOXIN | |||||||||
Biological species | Yersinia entomophaga (bacteria) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Sitsel O / Wang Z / Janning P / Kroczek L / Raunser S | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15405.map.gz | 195.9 MB | EMDB map data format | |
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Header (meta data) | emd-15405-v30.xml emd-15405.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | emd_15405.png | 237 KB | ||
Filedesc metadata | emd-15405.cif.gz | 4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15405 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15405 | HTTPS FTP |
-Validation report
Summary document | emd_15405_validation.pdf.gz | 398.9 KB | Display | EMDB validaton report |
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Full document | emd_15405_full_validation.pdf.gz | 398.5 KB | Display | |
Data in XML | emd_15405_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | emd_15405_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15405 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15405 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15405.map.gz / Format: CCP4 / Size: 210.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 11.872 Å | ||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Yersinia entomophaga strain Ara-YenR (YeEln/YeIspn/YeOspn KO)
Entire | Name: Yersinia entomophaga strain Ara-YenR (YeEln/YeIspn/YeOspn KO) |
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Components |
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-Supramolecule #1: Yersinia entomophaga strain Ara-YenR (YeEln/YeIspn/YeOspn KO)
Supramolecule | Name: Yersinia entomophaga strain Ara-YenR (YeEln/YeIspn/YeOspn KO) type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Yersinia entomophaga (bacteria) / Strain: Ara-YenR (YeEln/YeIspn/YeOspn KO) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 / Component - Concentration: 1.0 x / Component - Formula: PBS / Component - Name: Phosphate-Buffered Saline |
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Vitrification | Cryogen name: ETHANE |
Sectioning | Focused 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 marker | Manufacturer: Aurion / Diameter: 5 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 130.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Number images used: 37 |
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