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- EMDB-8850: Cryo-EM structure of B. subtilis flagellar filaments H84R -

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Basic information

Database: EMDB / ID: 8850
TitleCryo-EM structure of B. subtilis flagellar filaments H84R
SampleBacillus subtilis flagella filament
SourceBacillus subtilis / bacteria / /
Map dataCryo-EM structure of B. subtilis flagellar filaments H84R
Methodhelical reconstruction, at 4.4 Å resolution
AuthorsWang F / Burrage AM
CitationNat Commun, 2017, 8, 960-960

Nat Commun, 2017, 8, 960-960 Yorodumi Papers
A structural model of flagellar filament switching across multiple bacterial species.
Fengbin Wang / Andrew M Burrage / Sandra Postel / Reece E Clark / Albina Orlova / Eric J Sundberg / Daniel B Kearns / Edward H Egelman

Validation ReportPDB-ID: 5wjw

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: 0.35
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.35
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5wjw
  • Surface level: 0.35
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5wjw
  • Imaged by Jmol
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3D viewer
Supplemental images

Downloads & links


Fileemd_8850.map.gz (map file in CCP4 format, 353895 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
600 pix
1.05 Å/pix.
= 630. Å
384 pix
1.05 Å/pix.
= 403.2 Å
384 pix
1.05 Å/pix.
= 403.2 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.05 Å
Contour Level:0.35 (by author), 0.35 (movie #1):
Minimum - Maximum-0.51726735 - 0.97478753
Average (Standard dev.)0.011076903 (0.072549045)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA: 403.19998 Å / B: 403.19998 Å / C: 630 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z384384600
origin x/y/z0.0000.0000.000
length x/y/z403.200403.200630.000
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-192-192-300
D min/max/mean-0.5170.9750.011

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 / Recombinant expression: No
MassTheoretical: 32.680332 kDa
Source (engineered)Expression System: Bacillus subtilis / bacteria / /

Experimental details

Sample preparation

Specimen statefilament
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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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: 20 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: 4.4 Å / Resolution method: OTHER / Details: model-map FSC 0.38 cut-off

Atomic model buiding

Output model

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