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- PDB-1ucu: R-type straight flagellar filament made of full-length flagellin -

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Basic information

Entry
Database: PDB / ID: 1ucu
TitleR-type straight flagellar filament made of full-length flagellin
DescriptorFlagellin
KeywordsSTRUCTURAL PROTEIN / FLAGELLIN / FLAGELLAR FILAMENT / HELICAL RECONSTRUCTION / Structural protein
Specimen sourceSalmonella typhimurium / bacteria / サルモネラ・ティフィムリウム, ネズミチフス菌
MethodElectron microscopy (4 Å resolution / Filament / Helical)
AuthorsYonekura, K. / Maki-Yonekura, S. / Namba, K.
CitationNature, 2003, 424, 643-650

primary. Nature, 2003, 424, 643-650 Yorodumi Papers
Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy.
Koji Yonekura / Saori Maki-Yonekura / Keiichi Namba

#1. NATURE, 2001, 410, 331-337
Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling
Samatey, F.A. / Imada, K. / Nagashima, S. / Vonderviszt, F. / Kumasaka, T. / Yamamoto, M. / Namba, K.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 22, 2003 / Release: Aug 12, 2003
RevisionDateData content typeGroupProviderType
1.0Aug 12, 2003Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
Remark 244 OTHER_DETAILS: REPEAT DISTANCE (ANGSTROMS) : 1698.8 BASIC HELIX INDEX (N10, L10) : ( 11, 4) (N01, L01) : ( -5, 31) SELECTION RULE : L = 66 N + 361 M MAXIMUM BESSEL ORDER : 170 NUMBER OF LAYER-LINES : 298 NUMBER OF FILAMENT IMAGES : 102 NUMBER OF MOLECULAR IMAGES : 41,469 EFFECTIVE RESOLUTION (ANGSTROMS) : 4.000 ALONG THE MERIDIAN EFFECTIVE RESOLUTION (ANGSTROMS) : 5.000 ALONG THE EQUATOR
Remark 650HELIX Determination method: Author determined
Remark 700SHEET Determination method: Author determined

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Assembly

Deposited unit
A: phase 1 Flagellin


Theoretical massNumber of molelcules
Total (without water)51,5511
Polyers51,5511
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Polypeptide(L)phase 1 Flagellin


Mass: 51551.203 Da / Num. of mol.: 1 / Mutation: A449V
Source: (natural) Salmonella typhimurium / bacteria / サルモネラ・ティフィムリウム, ネズミチフス菌
References: UniProt: P06179

Cellular component

Molecular function

Biological process

  • bacterial-type flagellum-dependent cell motility (GO: 0071973)
  • MyD88-dependent toll-like receptor signaling pathway (GO: 0002755)
  • toll-like receptor 5 signaling pathway (GO: 0034146)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: HELICAL

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Sample preparation

ComponentName: R-TYPE STRAIGHT FLAGELLAR FILAMENT / Type: COMPLEX
Buffer solutionName: 150MM NACL, 2MM MGCL2, 20MM TRIS-HCL, 2-5% GLYCEROL
Details: 150MM NACL, 2MM MGCL2, 20MM TRIS-HCL, 2-5% GLYCEROL
pH: 7.8
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: QUANTIFOIL R1.2/1.3 (25 NM THICK)
Crystal grow
*PLUS
Temp unit: unknown / Method: unknown

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Electron microscopy imaging

MicroscopyMicroscope model: JEOL 3000SFF
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 / Calibrated magnification: 47600 / Nominal defocus max: 2200 nm / Nominal defocus min: 1100 nm / Cs: 1.6 mm
Specimen holderTemperature: 4 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

Software
NameClassification
FEX-PLORrefinement
FX-PLORrefinement
EM softwareName: X-PLOR / Category: MODEL FITTING
CTF correctionDetails: BOTH AMPLITUDE AND PHASE
3D reconstructionMethod: HELICAL RECONSTRUCTION / Resolution: 4 Å / Number of particles: 102 / Nominal pixel size: 1 / Actual pixel size: 1.05
Magnification calibration: R-TYPE STRAIGHT FLAGELLAR FILAMENT
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.
Symmetry type: HELICAL
Atomic model buildingDetails: REFINEMENT PROTOCOL--POSITIONAL AND SIMULATED ANNEALING
Ref protocol: FLEXIBLE FIT / Ref space: RECIPROCAL / Target criteria: amplitude-weighted phase residual
Atomic model buildingPDB-ID: 1IO1
Least-squares processR factor R work: 0.3 / Highest resolution: 4 Å / Lowest resolution: 30 Å
Refine hist #LASTHighest resolution: 4 Å / Lowest resolution: 30 Å
Number of atoms included #LASTProtein: 3617 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 3617

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