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Yorodumi- EMDB-40219: A subtomogram averaged structure of Helicobacter pylori flagellar... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40219 | ||||||||||||
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Title | A subtomogram averaged structure of Helicobacter pylori flagellar motor from a flgV deletion mutant. | ||||||||||||
Map data | A subtomogram averaged structure of H.pylori flagellar motor from dflgV. | ||||||||||||
Sample |
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Keywords | flagella / motor / H.pylori / MOTOR PROTEIN | ||||||||||||
Biological species | Helicobacter pylori B128 (bacteria) | ||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 31.0 Å | ||||||||||||
Authors | Liu J / Tachiyama S | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: PLoS One / Year: 2023 Title: FlgV forms a flagellar motor ring that is required for optimal motility of Helicobacter pylori. Authors: Jack M Botting / Shoichi Tachiyama / Katherine H Gibson / Jun Liu / Vincent J Starai / Timothy R Hoover / Abstract: Flagella-driven motility is essential for Helicobacter pylori to colonize the human stomach, where it causes a variety of diseases, including chronic gastritis, peptic ulcer disease, and gastric ...Flagella-driven motility is essential for Helicobacter pylori to colonize the human stomach, where it causes a variety of diseases, including chronic gastritis, peptic ulcer disease, and gastric cancer. H. pylori has evolved a high-torque-generating flagellar motor that possesses several accessories not found in the archetypical Escherichia coli motor. FlgV was one of the first flagellar accessory proteins identified in Campylobacter jejuni, but its structure and function remain poorly understood. Here, we confirm that deletion of flgV in H. pylori B128 and a highly motile variant of H. pylori G27 (G27M) results in reduced motility in soft agar medium. Comparative analyses of in-situ flagellar motor structures of wild-type, ΔflgV, and a strain expressing FlgV-YFP showed that FlgV forms a ring-like structure closely associated with the junction of two highly conserved flagellar components: the MS and C rings. The results of our studies suggest that the FlgV ring has adapted specifically in Campylobacterota to support the assembly and efficient function of the high-torque-generating motors. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40219.map.gz | 9.6 MB | EMDB map data format | |
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Header (meta data) | emd-40219-v30.xml emd-40219.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
Images | emd_40219.png | 90.6 KB | ||
Filedesc metadata | emd-40219.cif.gz | 4.1 KB | ||
Others | emd_40219_half_map_1.map.gz emd_40219_half_map_2.map.gz | 9.6 MB 9.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40219 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40219 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_40219.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | A subtomogram averaged structure of H.pylori flagellar motor from dflgV. | ||||||||||||||||||||
Voxel size | X=Y=Z: 8.592 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: A half map from the averaged structure of...
File | emd_40219_half_map_1.map | ||||||||||||
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Annotation | A half map from the averaged structure of H.pylori flagellar motor from dflgV. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: A half map from the averaged structure of...
File | emd_40219_half_map_2.map | ||||||||||||
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Annotation | A half map from the averaged structure of H.pylori flagellar motor from dflgV. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Helicobacter pylori flagellar motor from a flgV deletion mutant
Entire | Name: Helicobacter pylori flagellar motor from a flgV deletion mutant |
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Components |
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-Supramolecule #1: Helicobacter pylori flagellar motor from a flgV deletion mutant
Supramolecule | Name: Helicobacter pylori flagellar motor from a flgV deletion mutant type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Helicobacter pylori B128 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm |
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) / Detector mode: COUNTING / Average electron dose: 1.81 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Extraction | Number tomograms: 224 / Number images used: 653 |
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Final angle assignment | Type: OTHER |
Final reconstruction | Applied symmetry - Point group: C18 (18 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 31.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 9108 |