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- EMDB-3257: Subtomogram average of a non-piliated type IVa pilus machine in M... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3257 | |||||||||
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Title | Subtomogram average of a non-piliated type IVa pilus machine in Myxococcus xanthus cells with pilA knockout | |||||||||
![]() | Subtomogram average of a non-piliated type IVa pilus machine in Myxococcus xanthus cells with pilA knockout | |||||||||
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![]() | type IV pilus / motor / motility / adhesion | |||||||||
Biological species | ![]() | |||||||||
Method | subtomogram averaging / cryo EM | |||||||||
![]() | Chang YW / Rettberg LA / Treuner-Lange A / Iwasa J / Sogaard-Andersen L / Jensen GJ | |||||||||
![]() | ![]() Title: Architecture of the type IVa pilus machine. Authors: Yi-Wei Chang / Lee A Rettberg / Anke Treuner-Lange / Janet Iwasa / Lotte Søgaard-Andersen / Grant J Jensen / ![]() ![]() Abstract: Type IVa pili are filamentous cell surface structures observed in many bacteria. They pull cells forward by extending, adhering to surfaces, and then retracting. We used cryo-electron tomography of ...Type IVa pili are filamentous cell surface structures observed in many bacteria. They pull cells forward by extending, adhering to surfaces, and then retracting. We used cryo-electron tomography of intact Myxococcus xanthus cells to visualize type IVa pili and the protein machine that assembles and retracts them (the type IVa pilus machine, or T4PM) in situ, in both the piliated and nonpiliated states, at a resolution of 3 to 4 nanometers. We found that T4PM comprises an outer membrane pore, four interconnected ring structures in the periplasm and cytoplasm, a cytoplasmic disc and dome, and a periplasmic stem. By systematically imaging mutants lacking defined T4PM proteins or with individual proteins fused to tags, we mapped the locations of all 10 T4PM core components and the minor pilins, thereby providing insights into pilus assembly, structure, and function. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 7.6 KB 7.6 KB | Display Display | ![]() |
Images | ![]() ![]() | 79.9 KB 55.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3247C ![]() 3248C ![]() 3249C ![]() 3250C ![]() 3251C ![]() 3252C ![]() 3253C ![]() 3254C ![]() 3255C ![]() 3256C ![]() 3258C ![]() 3259C ![]() 3260C ![]() 3261C ![]() 3262C ![]() 3263C ![]() 3264C ![]() 3jc8C ![]() 3jc9C C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Subtomogram average of a non-piliated type IVa pilus machine in Myxococcus xanthus cells with pilA knockout | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 7.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Myxococcus xanthus DK1622 cells with the pilA gene knockout
Entire | Name: Myxococcus xanthus DK1622 cells with the pilA gene knockout |
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Components |
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-Supramolecule #1000: Myxococcus xanthus DK1622 cells with the pilA gene knockout
Supramolecule | Name: Myxococcus xanthus DK1622 cells with the pilA gene knockout type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Type IVa pilus
Supramolecule | Name: Type IVa pilus / type: organelle_or_cellular_component / ID: 1 / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | cell |
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Sample preparation
Vitrification | Cryogen name: ETHANE-PROPANE MIXTURE / Instrument: FEI VITROBOT MARK III |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GATAN / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Date | Dec 28, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 150 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 26000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Software - Name: IMOD, TOMO3D, PEET / Number subtomograms used: 70 |
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