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

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Basic information

Entry
Database: EMDB / ID: EMD-6716
TitleRing assembly of FliF-FliG fusion protein
Map dataRing assembly of FliF-FliG fusion protein
Sample
  • Complex: FliFG fusion ring
Function / homology
Function and homology information


bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / plasma membrane
Similarity search - Function
Flagellar motor switch protein FliG / Flagellar motor switch protein FliG, alpha-helical / Flagellar motor switch protein FliG, C-terminal / Flagellar motor switch protein FliG, N-terminal domain / Flagellar motor switch protein FliG, middle domain / FliG C-terminal domain / FliG middle domain / FliG N-terminal domain / Flagellar M-ring protein FliF / Flagellar M-ring C-terminal ...Flagellar motor switch protein FliG / Flagellar motor switch protein FliG, alpha-helical / Flagellar motor switch protein FliG, C-terminal / Flagellar motor switch protein FliG, N-terminal domain / Flagellar motor switch protein FliG, middle domain / FliG C-terminal domain / FliG middle domain / FliG N-terminal domain / Flagellar M-ring protein FliF / Flagellar M-ring C-terminal / Flagellar M-ring protein C-terminal / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
Flagellar motor switch protein FliG / Flagellar M-ring protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 25.0 Å
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.
History
DepositionMar 16, 2017-
Header (metadata) releaseApr 12, 2017-
Map releaseApr 12, 2017-
UpdateApr 12, 2017-
Current statusApr 12, 2017Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6716.png

Downloads & links

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Map

FileDownload / File: emd_6716.map.gz / Format: CCP4 / Size: 844.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRing assembly of FliF-FliG fusion protein
Voxel sizeX=Y=Z: 4.8 Å
Density
Contour LevelBy AUTHOR: 1. / Movie #1: 1
Minimum - Maximum-0.91259074 - 2.0935736
Average (Standard dev.)0.35862404 (±0.46696302)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-30-30-30
Dimensions606060
Spacing606060
CellA=B=C: 288.0 Å
α=β=γ: 90.0 °

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
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
Components
  • Complex: FliFG fusion ring

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Supramolecule #1: FliFG fusion ring

SupramoleculeName: FliFG fusion ring / type: complex / ID: 1 / Parent: 0 / Details: FliF-FliG fusion ring oligomer from Salmonella
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21
Molecular weightTheoretical: 2.5 MDa

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 8
StainingType: POSITIVE / Material: ammonium molybdate / Details: 8% (w/v) ammonium molybdate, 2% (w/v) trehalose
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeHITACHI EF2000
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 62500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 0.003 µm / Nominal defocus min: 0.0008 µm
Specialist opticsEnergy filter - Name: Hitachi gamma-type energy filter
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
TemperatureMin: 93.0 K / Max: 93.0 K
Image recordingFilm or detector model: GATAN MULTISCAN / Average electron dose: 2.0 e/Å2

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Image processing

Startup modelType of model: OTHER / Details: model by EMAN startCsym
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN (ver. 1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN (ver. 1)
Final reconstructionNumber classes used: 33 / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN (ver. 1) / Number images used: 3400

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