Database: PDB / ID: 1ucu|
|Title||R-type straight flagellar filament made of full-length flagellin|
|Keywords||Structural protein / FLAGELLIN / FLAGELLAR FILAMENT / HELICAL RECONSTRUCTION|
|Specimen source||Salmonella typhimurium / bacteria|
|Method||Electron microscopy (4 A resolution / Helical / Vitreous ice (cryo EM))|
|Authors||Yonekura, K. / Maki-Yonekura, S. / Namba, K.|
|Citation||Nature, 2003, 424, 643-650|
#1. NATURE, 2001, 410, 331-337
|Date||Deposition: Apr 22, 2003 / Release: Aug 12, 2003 / Last modification: Feb 24, 2009|
|3D viewer|| / |
Downloads & links
A: phase 1 Flagellin
51.6 kDa, 1 molecules
|#1||idetical with deposited unit / defined by author / Symmetry operations: (identity)x1|
|#1||polypeptide(L) / phase 1 Flagellin / Mutation: A449V / Source: Salmonella typhimurium (gene. exp.) / References: UniProt: P06179|
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Reconstruction method: HELICAL / Specimen type: VITREOUS ICE (CRYO EM)|
|Assembly of specimen||Name: R-TYPE STRAIGHT FLAGELLAR FILAMENT / Aggregation state: FILAMENT|
|Buffer solution||Name: 150MM NACL, 2MM MGCL2, 20MM TRIS-HCL, 2-5% GLYCEROL|
|Sample preparation||pH: 7.8 / Sample conc.: 0.1 mg/ml|
|Specimen support||Details: QUANTIFOIL R1.2/1.3 (25 NM THICK)|
Electron microscopy imaging
|Microscopy||Microscope model: JEOL JEM-3000SFF|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2000 e/A2 / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 47600 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1100 nm / Cs: 1.6 mm|
|Specimen holder||Temperature: 4 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.|
|Camera||Type: KODAK SO163 FILM|
|Software||Name: FEX-PLOR / Classification: refinement|
|Computing||Structure refinement: FX-PLOR|
|Image selection||Software name: FEX-PLOR / Number of particles: 102|
|3D reconstruction||Method: HELICAL RECONSTRUCTION / Resolution: 4 A / Nominal pixel size: 1 A/pix / Actual pixel size: 1.05 A/pix|
Magnification calibration: R-TYPE STRAIGHT FLAGELLAR FILAMENT
CTF correction method: BOTH AMPLITUDE AND PHASE
Details: The atomic model of a flagellin fragment F41 from Samatey et al (2001) NATURE 410 331-337 (PDB ENTRY 1IO1) was fitted to the density map using O. Then, initial model of full-length flagellin was built by tracing missing terminal chains. The model was refined using both positional and simulated annealing refinements, by a molecular dynamics refinement program, FEX-PLOR, which we developed based on FX-PLOR for EM image analysis of the helical assembly. The amplitude-weighted phase-residual was implemented as an effective potential energy. The layer-line amplitude distributions of the EM data were then scaled to the structure factors calculated from the model based on their radial amplitude profiles obtained by averaging the amplitudes within each resolution shell. The density map was calculated again, and model building and refinement were iterated.
|Atomic model building||Ref protocol: POSITIONAL AND SIMULATED ANNEALING / Ref space: RECIPROCAL / Target criteria: amplitude-weighted phase residual|
|Least-squares process||R factor R work: 0.3 / Highest resolution: 4 A / Lowest resolution: 30 A|
|Refine hist #LAST||Highest resolution: 4 A / Lowest resolution: 30 A|
|Number of atoms included #LAST||Protein: 3617 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 3617|
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