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- EMDB-6716: Ring assembly of FliF-FliG fusion protein -

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Basic information

Entry
Database: EMDB / ID: 6716
TitleRing assembly of FliF-FliG fusion protein
Map dataRing assembly of FliF-FliG fusion protein
SampleFliFG fusion ring
Function/homology| / |
Function and homology information
SourceSalmonella enterica subsp. enterica serovar typhimurium / / bacteria
MethodCryo EM / Negative stain / single particle reconstruction / 25 Å resolution
AuthorsSuzuki H / Yonekura K / Namba K
CitationJournal: J. Mol. Biol. / Year: 2004
Title: Structure of the rotor of the bacterial flagellar motor revealed by electron cryomicroscopy and single-particle image analysis.
Authors: Hirofumi Suzuki / Koji Yonekura / Keiichi Namba
Abstract: The FliF ring is the base for self-assembly of the bacterial flagellum and the FliF/FliG ring complex is the core of the rotor of the flagellar motor. We report the structures of these two ring ...The FliF ring is the base for self-assembly of the bacterial flagellum and the FliF/FliG ring complex is the core of the rotor of the flagellar motor. We report the structures of these two ring complexes obtained by electron cryomicroscopy and single-particle image analysis at 22A and 25A resolution, respectively. Direct comparison of these structures with the flagellar basal body made by superimposing the density maps on the central section reveals many interesting features, such as how the mechanically stable connection between the ring and the rod is formed, how directly FliF domains are involved in the near axial density of the basal body forming the proximal end of the central channel for a potential gating mechanism, some indication of flexibility in the connection of FliF and FliG, and structural and functional similarities to the head-to-tail connectors of bacteriophages.
DateDeposition: Mar 16, 2017 / Header (metadata) release: Apr 12, 2017 / Map release: Apr 12, 2017 / Last update: Apr 12, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF CHIMERA
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3D viewer
Supplemental images

Downloads & links

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Map

Fileemd_6716.map.gz (map file in CCP4 format, 865 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
60 pix
4.8 Å/pix.
= 288. Å
60 pix
4.8 Å/pix.
= 288. Å
60 pix
4.8 Å/pix.
= 288. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 4.8 Å
Density
Contour Level:1 (by author), 1 (movie #1):
Minimum - Maximum-0.91259074 - 2.0935736
Average (Standard dev.)0.35862404 (0.46696302)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions606060
Origin-30-30-30
Limit292929
Spacing606060
CellA=B=C: 288 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.84.84.8
M x/y/z606060
origin x/y/z0.0000.0000.000
length x/y/z288.000288.000288.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-30-30-30
NC/NR/NS606060
D min/max/mean-0.9132.0940.359

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Supplemental data

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Sample components

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Entire FliFG fusion ring

EntireName: FliFG fusion ring / Details: FliF-FliG fusion ring oligomer from Salmonella / Number of components: 1
MassTheoretical: 2.5 MDa

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Component #1: protein, FliFG fusion ring

ProteinName: FliFG fusion ring / Details: FliF-FliG fusion ring oligomer from Salmonella / Recombinant expression: No
MassTheoretical: 2.5 MDa
SourceSpecies: Salmonella enterica subsp. enterica serovar typhimurium / / bacteria
Source (engineered)Expression System: Escherichia coli / / bacteria / / Strain: BL21

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: Negative stain, Cryo EM
Sample solutionSpecimen conc.: 5 mg/ml / pH: 8
Staining8% (w/v) ammonium molybdate, 2% (w/v) trehalose
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: HITACHI EF2000
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 62500 X (calibrated) / Imaging mode: BRIGHT FIELD / Defocus: 0.8 - 3 nm / Energy filter: Hitachi gamma-type energy filter
Specimen HolderModel: OTHER / Temperature: K ( 93 - 93 K)
CameraDetector: GATAN MULTISCAN

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 3400
3D reconstructionSoftware: EMAN / Resolution: 25 Å / Resolution method: FSC 0.5 CUT-OFF

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