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Yorodumi- EMDB-1647: Specific arrangement of alpha-helical coiled coils in the core do... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1647 | |||||||||
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Title | Specific arrangement of alpha-helical coiled coils in the core domain of the bacterial flagellar hook for the universal joint function | |||||||||
Map data | This is a cryoEM map of the bacterial flagellar hook | |||||||||
Sample |
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Keywords | Bacterial flagellum / flagellar hook / universal joint / electron cryomicroscopy / 3D image reconstruction | |||||||||
Function / homology | Function and homology information bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum-dependent cell motility Similarity search - Function | |||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 7.1 Å | |||||||||
Authors | Fujii T / Kato T / Namba K | |||||||||
Citation | Journal: Structure / Year: 2009 Title: Specific arrangement of alpha-helical coiled coils in the core domain of the bacterial flagellar hook for the universal joint function. Authors: Takashi Fujii / Takayuki Kato / Keiichi Namba / Abstract: The bacterial flagellar hook is a short, highly curved tubular structure connecting the rotary motor to the filament acting as a helical propeller. The bending flexibility of the hook allows it to ...The bacterial flagellar hook is a short, highly curved tubular structure connecting the rotary motor to the filament acting as a helical propeller. The bending flexibility of the hook allows it to work as a universal joint. A partial atomic model of the hook revealed a sliding intersubunit domain interaction along the protofilament to produce bending flexibility. However, it remained unclear how the tightly packed inner core domains can still permit axial extension and compression. We report advances in cryoEM image analysis for high-resolution, high-throughput structural analysis and a density map of the hook that reveals most of the secondary structures, including the terminal alpha helices forming a coiled coil. The orientations and axial packing interactions of these two alpha helices are distinctly different from those of the filament, allowing them to have a room for axial compression and extension for bending flexibility without impairing the mechanical stability of the hook. | |||||||||
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_1647.map.gz | 28.6 MB | EMDB map data format | |
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Header (meta data) | emd-1647-v30.xml emd-1647.xml | 9.7 KB 9.7 KB | Display Display | EMDB header |
Images | 1647.jpg | 331.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1647 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1647 | HTTPS FTP |
-Validation report
Summary document | emd_1647_validation.pdf.gz | 398 KB | Display | EMDB validaton report |
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Full document | emd_1647_full_validation.pdf.gz | 397.5 KB | Display | |
Data in XML | emd_1647_validation.xml.gz | 6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1647 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1647 | HTTPS FTP |
-Related structure data
Related structure data | 3a69MC 6jztM M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_1647.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a cryoEM map of the bacterial flagellar hook | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.68 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 : Bacterial flagellar hook
Entire | Name: Bacterial flagellar hook |
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Components |
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-Supramolecule #1000: Bacterial flagellar hook
Supramolecule | Name: Bacterial flagellar hook / type: sample / ID: 1000 / Oligomeric state: Bacterial flagellar hook / Number unique components: 1 |
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-Macromolecule #1: Bacterial flagellar hook
Macromolecule | Name: Bacterial flagellar hook / type: protein_or_peptide / ID: 1 / Name.synonym: Bacterial flagellar hook / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7 / Details: 20mM Tris-HCl, 100mM NaCl |
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Grid | Details: Quantifoil holey carbon molybdenum grid R0.6/1.0 |
Vitrification | Cryogen name: HELIUM / Chamber humidity: 90 % / Chamber temperature: 4.6 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Vitorobot |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Temperature | Average: 50 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification |
Specialist optics | Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 10.0 eV |
Date | Feb 20, 2008 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 200 / Average electron dose: 20 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 89285 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.6 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Top entry liquid helium-cooled cryo specimen holder Specimen holder model: JEOL |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 4.12 Å Applied symmetry - Helical parameters - Δ&Phi: 64.78 ° Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER |
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CTF correction | Details: Each particle |