+Open data
-Basic information
Entry | Database: PDB / ID: 6jzr | ||||||||||||||||||
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Title | Structure of the bacterial flagellar polyrod | ||||||||||||||||||
Components | Flagellar basal-body rod protein FlgG | ||||||||||||||||||
Keywords | MOTOR PROTEIN / Bacterial flagellum / rod protein / STRUCTURAL PROTEIN | ||||||||||||||||||
Function / homology | Function and homology information bacterial-type flagellum basal body, distal rod / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum-dependent cell motility Similarity search - Function | ||||||||||||||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 7.4 Å | ||||||||||||||||||
Authors | Saijo-Hamano, Y. / Matsunami, H. / Namba, K. / Imada, K. | ||||||||||||||||||
Funding support | Japan, 5items
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Citation | Journal: Biomolecules / Year: 2019 Title: Architecture of the Bacterial Flagellar Distal Rod and Hook of . Authors: Yumiko Saijo-Hamano / Hideyuki Matsunami / Keiichi Namba / Katsumi Imada / Abstract: The bacterial flagellum is a large molecular complex composed of thousands of protein subunits for motility. The filamentous part of the flagellum, which is called the axial structure, consists of ...The bacterial flagellum is a large molecular complex composed of thousands of protein subunits for motility. The filamentous part of the flagellum, which is called the axial structure, consists of the filament, the hook, and the rods, with other minor components-the cap protein and the hook associated proteins. They share a common basic architecture of subunit arrangement, but each part shows quite distinct mechanical properties to achieve its specific function. The distal rod and the hook are helical assemblies of a single protein, FlgG and FlgE, respectively. They show a significant sequence similarity but have distinct mechanical characteristics. The rod is a rigid, straight cylinder, whereas the hook is a curved tube with high bending flexibility. Here, we report a structural model of the rod constructed by using the crystal structure of a core fragment of FlgG with a density map obtained previously by electron cryomicroscopy. Our structural model suggests that a segment called L-stretch plays a key role in achieving the distinct mechanical properties of the rod using a structurally similar component protein to that of the hook. | ||||||||||||||||||
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 | 6jzr.cif.gz | 870.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jzr.ent.gz | 742.9 KB | Display | PDB format |
PDBx/mmJSON format | 6jzr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jzr_validation.pdf.gz | 886.1 KB | Display | wwPDB validaton report |
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Full document | 6jzr_full_validation.pdf.gz | 908.8 KB | Display | |
Data in XML | 6jzr_validation.xml.gz | 121.4 KB | Display | |
Data in CIF | 6jzr_validation.cif.gz | 160.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/6jzr ftp://data.pdbj.org/pub/pdb/validation_reports/jz/6jzr | HTTPS FTP |
-Related structure data
Related structure data | 6683M 6jf2C 6jztC 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: 27826.887 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Source: (natural) Salmonella typhimurium (bacteria) / Variant: TH9709 / References: UniProt: A0A0J5DTL8, UniProt: P0A1J3*PLUS |
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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 enterica subsp. enterica serovar Typhimurium (bacteria) Strain: TH9709 |
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: 300 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
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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 | ||||||||||||||||||||||||
Refine LS restraints |
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