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Yorodumi- PDB-5wrh: FlgG structure based on the CryoEM map of the bacterial flagellar... -
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-Basic information
Entry | Database: PDB / ID: 5wrh | ||||||
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Title | FlgG structure based on the CryoEM map of the bacterial flagellar polyrod | ||||||
Components | Flagellar basal-body rod protein FlgG | ||||||
Keywords | MOTOR PROTEIN / the bacterial flagellar motor | ||||||
Function / homology | Function and homology information bacterial-type flagellum basal body, distal rod / bacterial-type flagellum-dependent swarming motility Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 7.4 Å | ||||||
Authors | Fujii, T. / Namba, K. | ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Identical folds used for distinct mechanical functions of the bacterial flagellar rod and hook. Authors: Takashi Fujii / Takayuki Kato / Koichi D Hiraoka / Tomoko Miyata / Tohru Minamino / Fabienne F V Chevance / Kelly T Hughes / Keiichi Namba / Abstract: The bacterial flagellum is a motile organelle driven by a rotary motor, and its axial portions function as a drive shaft (rod), a universal joint (hook) and a helical propeller (filament). The rod ...The bacterial flagellum is a motile organelle driven by a rotary motor, and its axial portions function as a drive shaft (rod), a universal joint (hook) and a helical propeller (filament). The rod and hook are directly connected to each other, with their subunit proteins FlgG and FlgE having 39% sequence identity, but show distinct mechanical properties; the rod is straight and rigid as a drive shaft whereas the hook is flexible in bending as a universal joint. Here we report the structure of the rod and comparison with that of the hook. While these two structures have the same helical symmetry and repeat distance and nearly identical folds of corresponding domains, the domain orientations differ by ∼7°, resulting in tight and loose axial subunit packing in the rod and hook, respectively, conferring the rigidity on the rod and flexibility on the hook. This provides a good example of versatile use of a protein structure in biological organisms. | ||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 5wrh.cif.gz | 40.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wrh.ent.gz | 29.6 KB | Display | PDB format |
PDBx/mmJSON format | 5wrh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wrh_validation.pdf.gz | 708.5 KB | Display | wwPDB validaton report |
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Full document | 5wrh_full_validation.pdf.gz | 738.2 KB | Display | |
Data in XML | 5wrh_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 5wrh_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/5wrh ftp://data.pdbj.org/pub/pdb/validation_reports/wr/5wrh | HTTPS FTP |
-Related structure data
Related structure data | 6683MC 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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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 22 / Rise per n subunits: 4.13 Å / Rotation per n subunits: 64.723 °) |
-Components
#1: Protein | Mass: 27784.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / References: UniProt: P0A1J3 |
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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: the bacterial flagellar polyrod / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: JEOL 3200FSC |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Helical symmerty | Angular rotation/subunit: 64.75 ° / Axial rise/subunit: 4.13 Å / Axial symmetry: C1 |
3D reconstruction | Resolution: 7.4 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 10645 / Symmetry type: HELICAL |