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Yorodumi- PDB-6jy0: CryoEM structure of S.typhimurium R-type straight flagellar filam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jy0 | ||||||
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Title | CryoEM structure of S.typhimurium R-type straight flagellar filament made of FljB (A461V) | ||||||
Components | Flagellin | ||||||
Keywords | PROTEIN FIBRIL / FljB / Helical reconstruction / Salmonella / Flagellar motor | ||||||
Function / homology | Function and homology information bacterial-type flagellum filament / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.56 Å | ||||||
Authors | Yamaguchi, T. / Toma, S. / Terahara, N. / Miyata, T. / Minamino, T. / Ashikara, M. / Namba, K. / Kato, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biomolecules / Year: 2020 Title: Structural and Functional Comparison of Flagellar Filaments Composed of FljB and FliC. Authors: Tomoko Yamaguchi / Shoko Toma / Naoya Terahara / Tomoko Miyata / Masamichi Ashihara / Tohru Minamino / Keiichi Namba / Takayuki Kato / Abstract: The bacterial flagellum is a motility organelle consisting of a long helical filament as a propeller and a rotary motor that drives rapid filament rotation to produce thrust. serovar Typhimurium has ...The bacterial flagellum is a motility organelle consisting of a long helical filament as a propeller and a rotary motor that drives rapid filament rotation to produce thrust. serovar Typhimurium has two genes of flagellin, and , for flagellar filament formation and autonomously switches their expression at a frequency of 10-10 per cell per generation. We report here differences in their structures and motility functions under high-viscosity conditions. A strain expressing FljB showed a higher motility than one expressing FliC under high viscosity. To examine the reasons for this motility difference, we carried out structural analyses of the FljB filament by electron cryomicroscopy and found that the structure was nearly identical to that of the FliC filament except for the position and orientation of the outermost domain D3 of flagellin. The density of domain D3 was much lower in FljB than FliC, suggesting that domain D3 of FljB is more flexible and mobile than that of FliC. These differences suggest that domain D3 plays an important role not only in changing antigenicity of the filament but also in optimizing motility function of the filament as a propeller under different conditions. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6jy0.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6jy0.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 6jy0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jy0_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6jy0_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 6jy0_validation.xml.gz | 350.8 KB | Display | |
Data in CIF | 6jy0_validation.cif.gz | 488 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/6jy0 ftp://data.pdbj.org/pub/pdb/validation_reports/jy/6jy0 | HTTPS FTP |
-Related structure data
Related structure data | 9896MC 0980C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 52608.449 Da / Num. of mol.: 22 / Mutation: A461V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Gene: fljB, C2253_13415, CET98_21075, D7F20_13880, D7H43_12410, DJ388_21755 Production host: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) References: UniProt: Q549S3 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: FljB / Type: COMPLEX / Details: R-type straight flagellar filament (A461V) / Entity ID: all / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: SJW590 | ||||||||||||||||||||
Source (recombinant) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||||||||||||||||
Buffer solution | pH: 7.8 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: MOLYBDENUM / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3 | ||||||||||||||||||||
EM embedding | Material: buffer | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Calibrated magnification: 72273 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 210 nm / Calibrated defocus max: 1600 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 10.3 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 2319 |
Image scans | Movie frames/image: 7 / Used frames/image: 1-6 |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | |||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | |||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 65.813 ° / Axial rise/subunit: 4.86758 Å / Axial symmetry: C1 | |||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 197442 | |||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114110 / Details: Half-map generation is Gold-standard / Symmetry type: HELICAL |