Bacterial Flagellar Structures

Bacterial Flagellar Structures
At Atomic Resolution
by Eric Martz at the Protonic Nanomachine Group (Osaka, Japan)
in collaboration with Fadel Samatey, Katsumi Imada, and Keiichi Namba.

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Contents

Movies
2001: Flagellar Monomer
2003: Flagellar Filanemt
2004: Flagellar Hook

Movies of Flagella & Flagellar Assembly.
- Movies of Salmonella Swimming, Motor Reversal
- Movie of Proposed Flagellar Assembly Mechanism (Movie Alone)
2001: Flagellar monomer 1IO1 (41 kD fragment 54-451, 2.0 Å) PubMed
Samatey, Imada, Nagashima, Vonderviszt, Kumasaka, Yamamoto, Namba
- Monomer (3,234 atoms): RCSB PDB / Proteopedia / FirstGlance in Jmol / Protein Explorer*
- Protofilament formed in the crystal -- Trimer (8,640 atoms): FirstGlance in Jmol / Protein Explorer*
- Stretching the Protofilament: Model for switching the protofilament to form left- vs. right-handed helical flagellar filaments. (L type repeat is 0.8 Å > R type). Simulated extension of the protofilament (jump at 4.5-5.0 Å extension; 16 models, total 137,136 atoms):
  - Animations in Chime*:
  - Animation in Protein Explorer*
2003: Flagellar filament.
Yonekura, Maki-Yonekura, Namba
- Monomer 1UCU (3,617 atoms) RCSB PDB / Proteopedia / FirstGlance in Jmol / Protein Explorer*
- Monomers Compared: 1IO1 (41 kD fragment) vs. 1UCU (full-length monomer fitted into filament):
  - Animations in Chime*
  - Conservation in 1UCU (in Chime* MolSlides, analysis with ConSurf)
    Caution: Done with a pre-release of ConSurf 3; not definitive; should be re-run in final ConSurf 3!
- Filament (contains 11 protofilaments)
  - "Long" model: Alpha-carbon atoms only (30,134 atoms in 61 monomers; protofilament length: 5-6 monomers): Protein Explorer*
  - Short model: (26 monomers; protofilament length: 2-3 monomers):
    - Alpha carbon atoms only: (12,844 atoms) Protein Explorer*
    - All atoms except hydrogen: (94,042 atoms) FirstGlance in Jmol / Protein Explorer*
  - Cut-away model: (6 of 11 protofilaments [5 removed]; 33 monomers; protofilament length: 5-6 monomers):
    - Alpha carbon atoms only: (16,302 atoms) Protein Explorer*
    - All atoms except hydrogen: (119,361 atoms) FirstGlance in Jmol / Protein Explorer*
  - Conservation in the Cut-Away Filament (MolSlides in Chime*; 5 protofilaments removed, leaving 6 out of 11)
    Caution: Done with a pre-release of ConSurf 3; not definitive; should be re-run in final ConSurf 3!
  - Contacts model: (9 monomers; central monomer has all within-filament contacts)
    - All atoms except hydrogen: (32,553 atoms) FirstGlance in Jmol / Protein Explorer*
  - Conservation of Contacts within the Filament (MolSlides in Chime*; 9 monomers, with central monomer displaying all filament contacts)
    Caution: Done with a pre-release of ConSurf 3; not definitive; should be re-run in final ConSurf 3!
2004: Flagellar Hook.
Samatey, Matsunami, Imada, Nagashima, Shaikn, Thomas, Chen, DeRosier, Kitao, Namba
- This study, visualizations, and the resulting data were made available in 2004 at The Bacterial Flagellar Hook: A Molecular Universal Joint (part of the Atlas of Macromolecules of Protein Explorer).

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