+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0467 | |||||||||
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Title | Shewanella oneidensis MR-1 bacterial flagellar motor | |||||||||
Map data | em-volume_P1 | |||||||||
Sample |
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Biological species | Shewanella oneidensis MR-1 (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 69.0 Å | |||||||||
Authors | Kaplan M / Ghosal D / Subramanian P / Oikonomou CO / Kjaer A / Pirbadian S / Ortega DR / Briegel A / El-Naggar MY / Jensen GJ | |||||||||
Citation | Journal: Elife / Year: 2019 Title: The presence and absence of periplasmic rings in bacterial flagellar motors correlates with stator type. Authors: Mohammed Kaplan / Debnath Ghosal / Poorna Subramanian / Catherine M Oikonomou / Andreas Kjaer / Sahand Pirbadian / Davi R Ortega / Ariane Briegel / Mohamed Y El-Naggar / Grant J Jensen / Abstract: The bacterial flagellar motor, a cell-envelope-embedded macromolecular machine that functions as a cellular propeller, exhibits significant structural variability between species. Different torque- ...The bacterial flagellar motor, a cell-envelope-embedded macromolecular machine that functions as a cellular propeller, exhibits significant structural variability between species. Different torque-generating stator modules allow motors to operate in different pH, salt or viscosity levels. How such diversity evolved is unknown. Here, we use electron cryo-tomography to determine the in situ macromolecular structures of three Gammaproteobacteria motors: , , and , providing the first views of intact motors with dual stator systems. Complementing our imaging with bioinformatics analysis, we find a correlation between the motor's stator system and its structural elaboration. Motors with a single H-driven stator have only the core periplasmic P- and L-rings; those with dual H-driven stators have an elaborated P-ring; and motors with Na or Na/H-driven stators have both their P- and L-rings embellished. Our results suggest an evolution of structural elaboration that may have enabled pathogenic bacteria to colonize higher-viscosity environments in animal hosts. #1: Journal: bioRxiv Title: The structural complexity of the Gammaproteobacteria flagellar motor is related to the type of its torque-generating stators Authors: Kaplan M / Ghosal D / Subramanian P / Oikonomou CO / Kjaer A / Pirbadian S / Ortega DR / El-Naggar MY / jensen GJ | |||||||||
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_0467.map.gz | 2.9 MB | EMDB map data format | |
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Header (meta data) | emd-0467-v30.xml emd-0467.xml | 8.6 KB 8.6 KB | Display Display | EMDB header |
Images | emd_0467.png | 59.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0467 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0467 | HTTPS FTP |
-Validation report
Summary document | emd_0467_validation.pdf.gz | 78.9 KB | Display | EMDB validaton report |
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Full document | emd_0467_full_validation.pdf.gz | 78.1 KB | Display | |
Data in XML | emd_0467_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0467 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0467 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0467.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | em-volume_P1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 19.2 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 : Shewanella oneidensis MR-1
Entire | Name: Shewanella oneidensis MR-1 (bacteria) |
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Components |
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-Supramolecule #1: Shewanella oneidensis MR-1
Supramolecule | Name: Shewanella oneidensis MR-1 / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Shewanella oneidensis MR-1 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 69.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 100 |
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Extraction | Number tomograms: 300 / Number images used: 100 |
Final angle assignment | Type: OTHER |