+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15403 | |||||||||
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Title | Structure of the secreted Yersinia entomophaga Tc toxin YenTc | |||||||||
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Sample |
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Keywords | Virulence / Secretion / Tc toxin / Type 10 secretion system / TOXIN | |||||||||
Biological species | Yersinia entomophaga (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 26.0 Å | |||||||||
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_15403.map.gz | 631.7 KB | EMDB map data format | |
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Header (meta data) | emd-15403-v30.xml emd-15403.xml | 14.5 KB 14.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15403_fsc.xml | 4.7 KB | Display | FSC data file |
Images | emd_15403.png | 27.7 KB | ||
Masks | emd_15403_msk_1.map | 3.8 MB | Mask map | |
Filedesc metadata | emd-15403.cif.gz | 4.1 KB | ||
Others | emd_15403_half_map_1.map.gz emd_15403_half_map_2.map.gz | 2.8 MB 2.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15403 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15403 | HTTPS FTP |
-Validation report
Summary document | emd_15403_validation.pdf.gz | 587.8 KB | Display | EMDB validaton report |
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Full document | emd_15403_full_validation.pdf.gz | 587.3 KB | Display | |
Data in XML | emd_15403_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | emd_15403_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15403 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15403 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15403.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 9.288 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15403_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15403_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15403_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
-Entire : Yersinia entomophaga strain Ara-YenR
Entire | Name: Yersinia entomophaga strain Ara-YenR |
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Components |
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-Supramolecule #1: Yersinia entomophaga strain Ara-YenR
Supramolecule | Name: Yersinia entomophaga strain Ara-YenR / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Yersinia entomophaga (bacteria) / Strain: Ara-YenR |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
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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Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 200 |
Vitrification | Cryogen name: ETHANE |
-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: 42000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |