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Yorodumi- EMDB-5313: Structural Diversity of Bacterial Flagellar Motors: Hyphomonas ne... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5313 | |||||||||
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Title | Structural Diversity of Bacterial Flagellar Motors: Hyphomonas neptunium | |||||||||
Map data | Final map is the C16-symmetrized average calculated from 27 individual sub-tomograms of Hyphomonas neptunium flagellar motors. | |||||||||
Sample |
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Keywords | Hyphomonas neptunium flagellar motor | |||||||||
Biological species | Hyphomonas neptunium (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / negative staining / Resolution: 68.0 Å | |||||||||
Authors | Chen S / Beeby M / Murphy GE / Leadbetter JR / Hendrixson DR / Briegel A / Li Z / Shi J / Tocheva EI / Muller A ...Chen S / Beeby M / Murphy GE / Leadbetter JR / Hendrixson DR / Briegel A / Li Z / Shi J / Tocheva EI / Muller A / Dobro MJ / Jensen GJ | |||||||||
Citation | Journal: EMBO J / Year: 2011 Title: Structural diversity of bacterial flagellar motors. Authors: Songye Chen / Morgan Beeby / Gavin E Murphy / Jared R Leadbetter / David R Hendrixson / Ariane Briegel / Zhuo Li / Jian Shi / Elitza I Tocheva / Axel Müller / Megan J Dobro / Grant J Jensen / Abstract: The bacterial flagellum is one of nature's most amazing and well-studied nanomachines. Its cell-wall-anchored motor uses chemical energy to rotate a microns-long filament and propel the bacterium ...The bacterial flagellum is one of nature's most amazing and well-studied nanomachines. Its cell-wall-anchored motor uses chemical energy to rotate a microns-long filament and propel the bacterium towards nutrients and away from toxins. While much is known about flagellar motors from certain model organisms, their diversity across the bacterial kingdom is less well characterized, allowing the occasional misrepresentation of the motor as an invariant, ideal machine. Here, we present an electron cryotomographical survey of flagellar motor architectures throughout the Bacteria. While a conserved structural core was observed in all 11 bacteria imaged, surprisingly novel and divergent structures as well as different symmetries were observed surrounding the core. Correlating the motor structures with the presence and absence of particular motor genes in each organism suggested the locations of five proteins involved in the export apparatus including FliI, whose position below the C-ring was confirmed by imaging a deletion strain. The combination of conserved and specially-adapted structures seen here sheds light on how this complex protein nanomachine has evolved to meet the needs of different species. | |||||||||
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_5313.map.gz | 1.2 MB | EMDB map data format | |
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Header (meta data) | emd-5313-v30.xml emd-5313.xml | 9.7 KB 9.7 KB | Display Display | EMDB header |
Images | emd_5313_1.png | 121.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5313 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5313 | HTTPS FTP |
-Validation report
Summary document | emd_5313_validation.pdf.gz | 78.3 KB | Display | EMDB validaton report |
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Full document | emd_5313_full_validation.pdf.gz | 77.4 KB | Display | |
Data in XML | emd_5313_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5313 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5313 | HTTPS FTP |
-Related structure data
Related structure data | 5297C 5298C 5299C 5300C 5308C 5309C 5310C 5311C 5312C 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_5313.map.gz / Format: CCP4 / Size: 1.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Final map is the C16-symmetrized average calculated from 27 individual sub-tomograms of Hyphomonas neptunium flagellar motors. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 15.48 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 : Hyphomonas neptunium flagellar motor
Entire | Name: Hyphomonas neptunium flagellar motor |
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Components |
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-Supramolecule #1000: Hyphomonas neptunium flagellar motor
Supramolecule | Name: Hyphomonas neptunium flagellar motor / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: flagellar motor
Supramolecule | Name: flagellar motor / type: organelle_or_cellular_component / ID: 1 / Name.synonym: flagellar motor / Number of copies: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Hyphomonas neptunium (bacteria) / Strain: ATCC 15444 |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | subtomogram averaging |
-Sample preparation
Buffer | Details: 2216 marine broth (Difco) |
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Staining | Type: NEGATIVE / Details: no staining |
Grid | Details: EM R2/2 copper/rhodium Quantifoil grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: OTHER / Details: Vitrification instrument: FEI Vitrobot |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Average: 82 K |
Specialist optics | Energy filter - Name: GATAN GIF / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Date | Jun 5, 2009 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Average electron dose: 200 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: 12.0 µm / Nominal defocus min: 8.0 µm / Nominal magnification: 27500 |
Sample stage | Specimen holder: FEI Polara / Specimen holder model: GATAN HELIUM / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | Average number of tilts used in the 3D reconstructions: 120. Average tomographic tilt angle increment: 1. |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 68.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD, Bsoft Details: Final map is the C16-symmetrized average calculated from 27 individual sub-tomograms. |