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Yorodumi- EMDB-11060: Flagellar motor of Shewanella putrefaciens in situ, flhG deletion -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11060 | |||||||||
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Title | Flagellar motor of Shewanella putrefaciens in situ, flhG deletion | |||||||||
Map data | Flagellar motor of Shewanella putrefaciens in situ, flhG deletion | |||||||||
Sample |
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Biological species | Shewanella putrefaciens CN-32 (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 79.0 Å | |||||||||
Authors | Blagotinsek V / Schwan M / Steinchen W / Mrusek D / Hook J / Rossmann FM / Freibert SA / Kressler D / Beeby M / Thormann KM / Bange G | |||||||||
Funding support | Germany, United Kingdom, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: An ATP-dependent partner switch links flagellar C-ring assembly with gene expression. Authors: Vitan Blagotinsek / Meike Schwan / Wieland Steinchen / Devid Mrusek / John C Hook / Florian Rossmann / Sven A Freibert / Hanna Kratzat / Guillaume Murat / Dieter Kressler / Roland Beckmann / ...Authors: Vitan Blagotinsek / Meike Schwan / Wieland Steinchen / Devid Mrusek / John C Hook / Florian Rossmann / Sven A Freibert / Hanna Kratzat / Guillaume Murat / Dieter Kressler / Roland Beckmann / Morgan Beeby / Kai M Thormann / Gert Bange / Abstract: Bacterial flagella differ in their number and spatial arrangement. In many species, the MinD-type ATPase FlhG (also YlxH/FleN) is central to the numerical control of bacterial flagella, and its ...Bacterial flagella differ in their number and spatial arrangement. In many species, the MinD-type ATPase FlhG (also YlxH/FleN) is central to the numerical control of bacterial flagella, and its deletion in polarly flagellated bacteria typically leads to hyperflagellation. The molecular mechanism underlying this numerical control, however, remains enigmatic. Using the model species , we show that FlhG links assembly of the flagellar C ring with the action of the master transcriptional regulator FlrA (named FleQ in other species). While FlrA and the flagellar C-ring protein FliM have an overlapping binding site on FlhG, their binding depends on the ATP-dependent dimerization state of FlhG. FliM interacts with FlhG independent of nucleotide binding, while FlrA exclusively interacts with the ATP-dependent FlhG dimer and stimulates FlhG ATPase activity. Our in vivo analysis of FlhG partner switching between FliM and FlrA reveals its mechanism in the numerical restriction of flagella, in which the transcriptional activity of FlrA is down-regulated through a negative feedback loop. Our study demonstrates another level of regulatory complexity underlying the spationumerical regulation of flagellar biogenesis and implies that flagellar assembly transcriptionally regulates the production of more initial building blocks. | |||||||||
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_11060.map.gz | 11.4 MB | EMDB map data format | |
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Header (meta data) | emd-11060-v30.xml emd-11060.xml | 12.1 KB 12.1 KB | Display Display | EMDB header |
Images | emd_11060.png | 320.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11060 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11060 | HTTPS FTP |
-Validation report
Summary document | emd_11060_validation.pdf.gz | 226.7 KB | Display | EMDB validaton report |
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Full document | emd_11060_full_validation.pdf.gz | 225.8 KB | Display | |
Data in XML | emd_11060_validation.xml.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11060 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11060 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_11060.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Flagellar motor of Shewanella putrefaciens in situ, flhG deletion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 8.28 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 : Flagellar motor of Shewanella putrefaciens in situ, wildtype
Entire | Name: Flagellar motor of Shewanella putrefaciens in situ, wildtype |
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Components |
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-Supramolecule #1: Flagellar motor of Shewanella putrefaciens in situ, wildtype
Supramolecule | Name: Flagellar motor of Shewanella putrefaciens in situ, wildtype type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Shewanella putrefaciens CN-32 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 / Component - Name: LB medium |
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Grid | Model: UltrAuFoil / Material: GOLD / Mesh: 200 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.02 kPa |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV Details: blot time 5 s, blot force 3, wait time 60s, drain time 0.5s,. |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Average exposure time: 1.5 sec. / Average electron dose: 3.15 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 25000 |
Sample stage | Specimen holder model: GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C100 (100 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 79.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET (ver. 1.10.1) / Number subtomograms used: 349 |
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Extraction | Number tomograms: 118 / Number images used: 349 / Reference model: sperical / Method: manual / Software - Name: PEET (ver. 1.10.1) |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: PEET (ver. 1.10.1) |