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- EMDB-8851: Cryo-EM structure of B. subtilis flagellar filaments S17P -

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Basic information

Entry
Database: EMDB / ID: 8851
TitleCryo-EM structure of B. subtilis flagellar filaments S17P
SampleBacillus subtilis flagella filament
SourceBacillus subtilis / bacteria / バチルス・サブティリス, 枯草菌 /
Map dataCryo-EM structure of B. subtilis flagellar filaments S17P
Methodhelical reconstruction, at 6.7 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: 5wjx

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

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.2
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 2.2
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5wjx
  • Surface level: 2.2
  • Imaged by UCSF CHIMERA
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5wjx
  • Imaged by Jmol
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Supplemental images

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Map

Fileemd_8851.map.gz (map file in CCP4 format, 88474 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
600 pix
1.05 Å/pix.
= 630. Å
192 pix
1.05 Å/pix.
= 201.6 Å
192 pix
1.05 Å/pix.
= 201.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.05 Å
Density
Contour Level:2.2 (by author), 2.2 (movie #1):
Minimum - Maximum-1.3625367 - 4.4867787
Average (Standard dev.)0.4876531 (0.8884126)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192600
Origin-96-96-300
Limit9595299
Spacing192192600
CellA: 201.59999 Å / B: 201.59999 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/z192192600
origin x/y/z0.0000.0000.000
length x/y/z201.600201.600630.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-96-96-300
NC/NR/NS192192600
D min/max/mean-1.3634.4870.488

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Supplemental data

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Sample components

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Entire Bacillus subtilis flagella filament

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

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Component #1: protein, Bacillus subtilis flagella filament

ProteinName: Bacillus subtilis flagella filament / Recombinant expression: No
SourceSpecies: Bacillus subtilis / bacteria / バチルス・サブティリス, 枯草菌 /
Source (engineered)Expression System: Bacillus subtilis / bacteria / バチルス・サブティリス, 枯草菌 /

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Component #2: protein, Flagellin

ProteinName: Flagellin / Recombinant expression: No
MassTheoretical: 32.67132 kDa
Source (engineered)Expression System: Bacillus subtilis / bacteria / バチルス・サブティリス, 枯草菌 /

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Experimental details

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Sample preparation

Specimen statefilament
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 4.68 Å / Delta phi: 65.29 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 %

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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)

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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).

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: BACK PROJECTION / Software: SPIDER / Resolution: 6.7 Å / Resolution method: OTHER / Details: model-map FSC 0.38 cut-off

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Atomic model buiding

Output model

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External links: The 2017 Nobel Prize in Chemistry - Press Release

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