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Yorodumi- EMDB-8460: In situ structure of chemoreceptor array from Helicobacter pylori... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8460 | ||||||||||||
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Title | In situ structure of chemoreceptor array from Helicobacter pylori using cryo-electron tomography | ||||||||||||
Map data | In situ structure of Chemoreceptor array from Helicobacter pylori using cryo-electron tomography, C6-symmetrized average from 677 subtomograms. | ||||||||||||
Sample |
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Biological species | Helicobacter pylori (bacteria) | ||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 41.0 Å | ||||||||||||
Authors | Qin Z / Liu J | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: J Bacteriol / Year: 2017 Title: Imaging the motility and chemotaxis machineries in Helicobacter pylori by cryo-electron tomography. Authors: Zhuan Qin / Wei-Ting Lin / Shiwei Zhu / Aime T Franco / Jun Liu / Abstract: Helicobacter pylori is a bacterial pathogen that can cause many gastrointestinal diseases including ulcers and gastric cancer. A unique chemotaxis-mediated motility is critical for H. pylori to ...Helicobacter pylori is a bacterial pathogen that can cause many gastrointestinal diseases including ulcers and gastric cancer. A unique chemotaxis-mediated motility is critical for H. pylori to colonize in the human stomach and to establish chronic infection, but the underlying molecular mechanisms are not well understood. Here we employ cryo-electron tomography to reveal detailed structures of the H. pylori cell envelope including the sheathed flagella and chemotaxis arrays. Notably, H. pylori possesses a distinctive periplasmic cage-like structure with 18-fold symmetry. We propose that this structure forms a robust platform for recruiting 18 torque generators, which likely provide the higher torque needed for swimming in high-viscosity environments. We also reveal a series of key flagellar assembly intermediates, providing structural evidence that flagellar assembly is tightly coupled with biogenesis of the membrane sheath. Finally, we determine the structure of putative chemotaxis arrays at the flagellar pole, which have implications for how direction of flagellar rotation is regulated. Together, our pilot cryo-ET studies provide novel structural insights into the unipolar flagella of H. pylori and lay a foundation for a better understanding of the unique motility of this organism. IMPORTANCE: Helicobacter pylori is a highly motile bacterial pathogen that colonizes approximately 50% of the world's population. H. pylori can move readily within the viscous mucosal layer of the ...IMPORTANCE: Helicobacter pylori is a highly motile bacterial pathogen that colonizes approximately 50% of the world's population. H. pylori can move readily within the viscous mucosal layer of the stomach. It has become increasingly clear that its unique flagella-driven motility is essential for successful gastric colonization and pathogenesis. Here we use advanced imaging techniques to visualize novel in situ structures with unprecedented detail in intact H. pylori cells. Remarkably, H. pylori possesses multiple unipolar flagella, which are driven by one of the largest flagellar motors found in bacteria. These large motors presumably provide higher torque needed by the bacterial pathogens to navigate in viscous environment of the human stomach. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8460.map.gz | 1.6 MB | EMDB map data format | |
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Header (meta data) | emd-8460-v30.xml emd-8460.xml | 8.6 KB 8.6 KB | Display Display | EMDB header |
Images | emd_8460.png | 97.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8460 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8460 | HTTPS FTP |
-Validation report
Summary document | emd_8460_validation.pdf.gz | 78.8 KB | Display | EMDB validaton report |
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Full document | emd_8460_full_validation.pdf.gz | 77.9 KB | Display | |
Data in XML | emd_8460_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8460 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8460 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8460.map.gz / Format: CCP4 / Size: 1.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | In situ structure of Chemoreceptor array from Helicobacter pylori using cryo-electron tomography, C6-symmetrized average from 677 subtomograms. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 8.91 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Chemoreceptor array in Helicobacter pylori, C6-symmetrized
Entire | Name: Chemoreceptor array in Helicobacter pylori, C6-symmetrized |
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Components |
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-Supramolecule #1: Chemoreceptor array in Helicobacter pylori, C6-symmetrized
Supramolecule | Name: Chemoreceptor array in Helicobacter pylori, C6-symmetrized type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Details: wild-type |
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Source (natural) | Organism: Helicobacter pylori (bacteria) / Strain: 7.13 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 41.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 677 |
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Extraction | Number tomograms: 19 / Number images used: 3000 |
Final angle assignment | Type: OTHER |