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Yorodumi- EMDB-40406: In situ structure of Helicobacter pylori flagellar motor from Pil... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40406 | |||||||||
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Title | In situ structure of Helicobacter pylori flagellar motor from PilN and PilO deletion mutant | |||||||||
Map data | A subtomogram averaged structure of Helicobacter pylori flagellar motor from PilN and PilO deletion mutant | |||||||||
Sample |
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Keywords | H.pylori / Flagella / PilN / PilO / MOTOR PROTEIN | |||||||||
Biological species | Helicobacter pylori G27 (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 39.0 Å | |||||||||
Authors | Tachiyama S / Liu J | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2024 Title: Bacterial flagella hijack type IV pili proteins to control motility. Authors: Xiaolin Liu / Shoichi Tachiyama / Xiaotian Zhou / Rommel A Mathias / Sharmin Q Bonny / Mohammad F Khan / Yue Xin / Anna Roujeinikova / Jun Liu / Karen M Ottemann / Abstract: Bacterial flagella and type IV pili (TFP) are surface appendages that enable motility and mechanosensing through distinct mechanisms. These structures were previously thought to have no components in ...Bacterial flagella and type IV pili (TFP) are surface appendages that enable motility and mechanosensing through distinct mechanisms. These structures were previously thought to have no components in common. Here, we report that TFP and some flagella share proteins PilO, PilN, and PilM, which we identified as part of the flagellar motor. mutants lacking PilO or PilN migrated better than wild type in semisolid agar because they continued swimming rather than aggregated into microcolonies, mimicking the TFP-regulated surface response. Like their TFP homologs, flagellar PilO/PilN heterodimers formed a peripheral cage that encircled the flagellar motor. These results indicate that PilO and PilN act similarly in flagella and TFP by differentially regulating motility and microcolony formation when bacteria encounter surfaces. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40406.map.gz | 6 MB | EMDB map data format | |
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Header (meta data) | emd-40406-v30.xml emd-40406.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
Images | emd_40406.png | 79.6 KB | ||
Filedesc metadata | emd-40406.cif.gz | 4.2 KB | ||
Others | emd_40406_half_map_1.map.gz emd_40406_half_map_2.map.gz | 6 MB 6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40406 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40406 | HTTPS FTP |
-Validation report
Summary document | emd_40406_validation.pdf.gz | 877 KB | Display | EMDB validaton report |
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Full document | emd_40406_full_validation.pdf.gz | 876.5 KB | Display | |
Data in XML | emd_40406_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | emd_40406_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40406 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40406 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_40406.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | A subtomogram averaged structure of Helicobacter pylori flagellar motor from PilN and PilO deletion mutant | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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: An EM half map of Helicobacter pylori flagellar...
File | emd_40406_half_map_1.map | ||||||||||||
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Annotation | An EM half map of Helicobacter pylori flagellar motor from PilN and PilO deletion mutant | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: An EM half map of Helicobacter pylori flagellar...
File | emd_40406_half_map_2.map | ||||||||||||
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Annotation | An EM half map of Helicobacter pylori flagellar motor from PilN and PilO deletion mutant | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Helicobacter pylori
Entire | Name: Helicobacter pylori (bacteria) |
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Components |
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-Supramolecule #1: Helicobacter pylori
Supramolecule | Name: Helicobacter pylori / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Helicobacter pylori G27 (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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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: 1.81 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C18 (18 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 39.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 6928 |
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Extraction | Number tomograms: 166 / Number images used: 478 |
Final angle assignment | Type: OTHER |