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R-type straight flagellar filament made of full-length flagellin

by helical reconstruction, at 4 A resolution

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Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 1ucu
TitleR-type straight flagellar filament made of full-length flagellin
DescriptorFlagellin
KeywordsStructural protein, FLAGELLIN, FLAGELLAR FILAMENT, HELICAL RECONSTRUCTION
AuthorsYonekura, K., Maki-Yonekura, S., Namba, K.
DateDeposition: 2003-04-22, Release: 2003-08-12
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
MoviesMovie Page

#1: Deposited structure unit, Image by Jmol

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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Article
Citation - primary
ArticleNature, Vol. 424, Issue 6949, Page 643-50, Year 2003
TitleComplete atomic model of the bacterial flagellar filament by electron cryomicroscopy.
AuthorsKoji Yonekura, Saori Maki-Yonekura, Keiichi Namba
Protonic NanoMachine Project, ERATO, JST.
KeywordsCryoelectron Microscopy, Crystallography, X-Ray, Flagella (chemistry), Flagellin (chemistry, 12777-81-0), Hydrophobic and Hydrophilic Interactions, Models, Molecular, Mutation, Missense, Protein Structure, Quaternary, Protein Structure, Tertiary, Protein Subunits, Salmonella typhimurium (chemistry), Static Electricity
LinksPubMed: 12904785, DOI: 10.1038/nature01830
Citation - 1
ArticleNATURE, Vol. 410, Page: 331 - 337, Year: 2001,
TitleStructure of the bacterial flagellar protofilament and implications for a switch for supercoiling
AuthorsSamatey, F.A., Imada, K., Nagashima, S., Vonderviszt, F., Kumasaka, T., Yamamoto, M., Namba, K.
Components
ID 1 : phase 1 Flagellin
Image
Descriptionphase 1 Flagellin
Typepolypeptide(L)
MutationA449V
Formula weight51551.785 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
Genus: Salmonella
NCBI taxonomy: ID:602
Organism scientific: Salmonella typhimurium
Strain: SJW 1665
LinksUniProt: P06179, Sequence view
Sample
Assembly
Aggregation stateFILAMENT
NameR-TYPE STRAIGHT FLAGELLAR FILAMENT
Buffer
Name150MM NACL, 2MM MGCL2, 20MM TRIS-HCL, 2-5% GLYCEROL
Experiment
Reconstruction methodHELICAL
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.8
Sample concentration0.1 mg/ml
Sample support
DetailsQUANTIFOIL R1.2/1.3 (25 NM THICK)
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: JEOL JEM-3000SFF
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Electron dose2000 e/A**2
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 47600 X, Nominal: 50000 X
CsNominal: 1.6 mm
Nominal defocusMax: 2200 nm, Min: 1100 nm
Specimen holder
Tilt angleMin: 0 degrees, Max: 0 degrees
Temperature4 Kelvin
Detector
TypeKODAK SO163 FILM
Processing
2D projection selection
Number of particles102
Software nameFEX-PLOR
3D reconstruction
Actual pixel size1.05 A/pix
CTF correction methodBOTH AMPLITUDE AND PHASE
DetailsThe 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.
Magnification calibrationR-TYPE STRAIGHT FLAGELLAR FILAMENT
MethodHELICAL RECONSTRUCTION
Nominal pixel size1.0 A/pix
Resolution4.000 A
3D fitting
Refinement ProtocolPOSITIONAL AND SIMULATED ANNEALING
Refinement SpaceRECIPROCAL
Target criteriaamplitude-weighted phase residual
3D fitting list
3D Fitting ID1
Computing
Structure refinementFX-PLOR
Refine
Refine idELECTRON MICROSCOPY
Ls R factor R work0.3
Ls d res high4.0 A
Ls d res low30 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high4.0
D res low30
Total atoms3617
Protein atoms3617
Software
Ordinal1
Classificationrefinement
NameFEX-PLOR
Download
PDB format
Allpdb1ucu.ent.gz
pdb1ucu.ent (uncompressed file)
Header onlypdb1ucu.ent.gz
mmCIF format
mmCIF1ucu.cif.gz
XML format
All1ucu.xml.gz
No-atom1ucu-noatom.xml.gz
Ext-atom1ucu-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.4 MB
.webm (WebM/VP8 format), 3.4 MB