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- EMDB-2521: Flagellar hook basal body in the tomogram of Salmonella mini-cell -

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Basic information

Entry
Database: EMDB / ID: EMD-2521
TitleFlagellar hook basal body in the tomogram of Salmonella mini-cell
Map dataFlagellar hook basal body from Salmonella mini-cell
Sample
  • Sample: Flagellar hook basal body from Salmonella typhimurium mini-cell in situ
  • Organelle or cellular component: flagellar hook basal body
KeywordsFlagellar motor / Type III secretion system / Salmonella typhimurium
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 45.0 Å
AuthorsKawamoto A / Morimoto VY / Miyata T / Minamino T / Hughes TK / Kato T / Namba K
CitationJournal: Sci Rep / Year: 2013
Title: Common and distinct structural features of Salmonella injectisome and flagellar basal body.
Authors: Akihiro Kawamoto / Yusuke V Morimoto / Tomoko Miyata / Tohru Minamino / Kelly T Hughes / Takayuki Kato / Keiichi Namba /
Abstract: Bacterial pathogens use an injectisome to deliver virulence proteins into eukaryotic host cells. The bacterial flagellum and injectisome export their component proteins for self-assembly. These two ...Bacterial pathogens use an injectisome to deliver virulence proteins into eukaryotic host cells. The bacterial flagellum and injectisome export their component proteins for self-assembly. These two systems show high structural similarities and are classified as the type III secretion system, but it remains elusive how similar they are in situ because the structures of these complexes isolated from cells and visualized by electron cryomicroscopy have shown only the export channel and housing for the export apparatus. Here we report in situ structures of Salmonella injectisome and flagellum by electron cryotomography. The injectisome lacks the flagellar basal body C-ring, but a wing-like disc and a globular density corresponding to the export gate platform and ATPase hexamer ring, respectively, are stably attached through thin connectors, revealing yet unidentified common architectures of the two systems. The ATPase ring is far from the disc, suggesting that both apparatuses are observed in an export-off state.
History
DepositionNov 26, 2013-
Header (metadata) releaseDec 18, 2013-
Map releaseDec 25, 2013-
UpdateDec 25, 2013-
Current statusDec 25, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0952
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0952
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2521-1.png

Downloads & links

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Map

FileDownload / File: emd_2521.map.gz / Format: CCP4 / Size: 2.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFlagellar hook basal body from Salmonella mini-cell
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
11.4 Å/pix.
x 82 pix.
= 934.8 Å		11.4 Å/pix.
x 82 pix.
= 934.8 Å		11.4 Å/pix.
x 82 pix.
= 934.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 11.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0952 / Movie #1: 0.0952
Minimum - Maximum-2.05901718 - 4.54621983
Average (Standard dev.)0.01755546 (±0.88184667)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin677-234-49
Dimensions828282
Spacing828282
CellA=B=C: 934.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z11.411.411.4
M x/y/z828282
origin x/y/z0.0000.0000.000
length x/y/z934.800934.800934.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-234677-49
NC/NR/NS828282
D min/max/mean-2.0594.5460.018

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Supplemental data

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Sample components

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Entire : Flagellar hook basal body from Salmonella typhimurium mini-cell i...

EntireName: Flagellar hook basal body from Salmonella typhimurium mini-cell in situ
Components
  • Sample: Flagellar hook basal body from Salmonella typhimurium mini-cell in situ
  • Organelle or cellular component: flagellar hook basal body

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Supramolecule #1000: Flagellar hook basal body from Salmonella typhimurium mini-cell i...

SupramoleculeName: Flagellar hook basal body from Salmonella typhimurium mini-cell in situ
type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: flagellar hook basal body

SupramoleculeName: flagellar hook basal body / type: organelle_or_cellular_component / ID: 1 / Name.synonym: flagellar motor / Recombinant expression: No
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Location in cell: Plasma membrane

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferDetails: M9 medium (17.1g Na2HPO4-12H2O, 3g KH2PO4, 0.5g NaCl, 1g NH4Cl, 0.2%glycerol, 1% tryptone, 1mM MgSO4 per litre)
GridDetails: Quantifoil molybdenum 200 mesh R0.6/1.0 grid with thin carbon support
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80 K
DateDec 6, 2012
Image recordingCategory: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Average electron dose: 200 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49030 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 7.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -70 ° / Tilt series - Axis1 - Max angle: 70 °
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C26 (26 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 45.0 Å / Resolution method: OTHER / Software - Name: EMAN / Number subtomograms used: 48

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