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Yorodumi- EMDB-3813: Tomogram of the salmonella enterica wild-type bacterial flagellar... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3813 | |||||||||
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Title | Tomogram of the salmonella enterica wild-type bacterial flagellar motor | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Salmonella (bacteria) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Beeby M / Ribardo DA / Brennan CA / Ruby EG / Jensen GJ / Hendrixson DR | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2016 Title: Diverse high-torque bacterial flagellar motors assemble wider stator rings using a conserved protein scaffold. Authors: Morgan Beeby / Deborah A Ribardo / Caitlin A Brennan / Edward G Ruby / Grant J Jensen / David R Hendrixson / Abstract: Although it is known that diverse bacterial flagellar motors produce different torques, the mechanism underlying torque variation is unknown. To understand this difference better, we combined genetic ...Although it is known that diverse bacterial flagellar motors produce different torques, the mechanism underlying torque variation is unknown. To understand this difference better, we combined genetic analyses with electron cryo-tomography subtomogram averaging to determine in situ structures of flagellar motors that produce different torques, from Campylobacter and Vibrio species. For the first time, to our knowledge, our results unambiguously locate the torque-generating stator complexes and show that diverse high-torque motors use variants of an ancestrally related family of structures to scaffold incorporation of additional stator complexes at wider radii from the axial driveshaft than in the model enteric motor. We identify the protein components of these additional scaffold structures and elucidate their sequential assembly, demonstrating that they are required for stator-complex incorporation. These proteins are widespread, suggesting that different bacteria have tailored torques to specific environments by scaffolding alternative stator placement and number. Our results quantitatively account for different motor torques, complete the assignment of the locations of the major flagellar components, and provide crucial constraints for understanding mechanisms of torque generation and the evolution of multiprotein complexes. | |||||||||
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_3813.map.gz | 244.5 MB | EMDB map data format | |
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Header (meta data) | emd-3813-v30.xml emd-3813.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | emd_3813.png | 146.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3813 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3813 | HTTPS FTP |
-Validation report
Summary document | emd_3813_validation.pdf.gz | 206.4 KB | Display | EMDB validaton report |
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Full document | emd_3813_full_validation.pdf.gz | 205.2 KB | Display | |
Data in XML | emd_3813_validation.xml.gz | 4.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3813 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3813 | HTTPS FTP |
-Related structure data
Related structure data | 3150C 3154C 3155C 3156C 3157C 3158C 3159C 3160C 3161C 3162C C: citing same article (ref.) |
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EM raw data | EMPIAR-10111 (Title: Tilt-series of salmonella enterica wild-type bacterial flagellar motor Data size: 328.0 MB Data #1: Tilt-series for salmonella enterica wild-type bacterial flagellar motor [tilt series]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3813.map.gz / Format: CCP4 / Size: 400 MB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 8.122 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 : Salmonella enterica Flagellar motor
Entire | Name: Salmonella enterica Flagellar motor |
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Components |
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-Supramolecule #1: Salmonella enterica Flagellar motor
Supramolecule | Name: Salmonella enterica Flagellar motor / type: organelle_or_cellular_component / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Salmonella (bacteria) / Strain: TH16943 / Location in cell: Cell wall |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 Details: PH is not know. PH of 7 was added because PH is a mandatory item. |
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Grid | Model: Quantifoil R2/2 / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE Details: Quantifoil R2/2 grids (200-mesh) (Quantifoil Micro Tools GmbH) were glow-discharged for 60 s at 10 mA. |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III |
Details | Salmonella strain TH16943 (ParaftsZ) was grown aerobically overnight in LB broth from freezer stocks at 37C. After overnight culture, 50 uL of 5% (wt/vol) L-arabinose were added to 5 mL fresh LB broth for each culture, and cultures were incubated for an additional 5 h. To enrich for minicells, 3 mL this culture were spun at 6,000 x g for 5 min, and the supernatant was recovered. The supernatant was spin-concentrated by centrifugation at 18,000 x g for 5 min, and the resultant pellet was resuspended in 50 uL LB broth and was immediately plunge-frozen. |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: Sigma-Aldrich / Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TECNAI 20 |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Dimensions - Width: 1024 pixel / Digitization - Dimensions - Height: 1024 pixel / Number grids imaged: 1 / Average electron dose: 0.6 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus min: 4.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 10.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER |
-Image processing
Final reconstruction | Resolution method: OTHER / Software: (Name: IMOD, RAPTOR, Leginon) / Number images used: 201 |
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CTF correction | Software - Name: TOMOCTF Software - details: High-defocus datasets were contrast transfer function (CTF)-corrected |