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- EMDB-8849: Cryo-EM structure of B. subtilis flagellar filaments A233V -

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Basic information

Database: EMDB / ID: 8849
TitleCryo-EM structure of B. subtilis flagellar filaments A233V
Map dataCryo-EM structure of B. subtilis flagellar filaments A233V
SampleBacillus subtilis flagella filament:
Function / homologyFlagellin, D0/D1 domain / Flagellin / Bacterial flagellin N-terminal helical region / Bacterial flagellin C-terminal helical region / bacterial-type flagellum filament / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region / Flagellin
Function and homology information
SourceBacillus subtilis (bacteria)
Methodhelical reconstruction / cryo EM / 5.5 Å resolution
AuthorsWang F / Burrage AM / Kearns DB / Egelman EH
CitationJournal: Nat Commun / Year: 2017
Title: A structural model of flagellar filament switching across multiple bacterial species.
Authors: Fengbin Wang / Andrew M Burrage / Sandra Postel / Reece E Clark / Albina Orlova / Eric J Sundberg / Daniel B Kearns / Edward H Egelman
Validation ReportPDB-ID: 5wjv

SummaryFull reportAbout validation report
DateDeposition: Jul 24, 2017 / Header (metadata) release: Aug 30, 2017 / Map release: Oct 25, 2017 / Last update: Nov 1, 2017

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 133
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 133
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5wjv
  • Surface level: 133
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5wjv
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_8849.map.gz (map file in CCP4 format, 536871 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.05 Å/pix.
= 537.6 Å
512 pix
1.05 Å/pix.
= 537.6 Å
512 pix
1.05 Å/pix.
= 537.6 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Contour Level:133.0 (by author), 133 (movie #1):
Minimum - Maximum-533.470100000000002 - 774.557559999999967
Average (Standard dev.)-11.027098000000001 (34.0458)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 537.6 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z537.600537.600537.600
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-256-256-256
D min/max/mean-533.470774.558-11.027

Supplemental data

Sample components

Entire Bacillus subtilis flagella filament

EntireName: Bacillus subtilis flagella filament / Number of components: 2

Component #1: protein, Bacillus subtilis flagella filament

ProteinName: Bacillus subtilis flagella filament / Recombinant expression: No
SourceSpecies: Bacillus subtilis (bacteria)
Source (engineered)Expression System: Bacillus subtilis (bacteria)

Component #2: protein, Flagellin

ProteinName: Flagellin / Number of Copies: 46 / Recombinant expression: No
MassTheoretical: 32.689336 kDa
SourceSpecies: Bacillus subtilis (bacteria)
Source (engineered)Expression System: Bacillus subtilis (bacteria)

Experimental details

Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 4.64 Å / Delta phi: 65.81 deg.
Sample solutionSpecimen conc.: 0.1 mg/ml / Buffer solution: Imidazole buffer / pH: 6.8
VitrificationCryogen name: ETHANE / Humidity: 90 %

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

Image acquisition

Image acquisitionDetails: Images were stored containing seven parts, where each part represented a set of frames corresponding to a dose of ~20 electrons per Angstrom^2. The full dose image stack was used for the estimation of the CTF as well as for boxing filaments. Only the first two parts were used for the reconstruction (~5 electrons per Angstrom^2).

Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: BACK PROJECTION / Software: SPIDER / Resolution: 5.5 Å / Resolution method: OTHER / Details: model-map FSC 0.38 cut-off

Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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