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- EMDB-1887: Flagellar basal body - Salmonella Typhimurium. -

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Basic information

Entry
Database: EMDB / ID: EMD-1887
TitleFlagellar basal body - Salmonella Typhimurium.
Map data34-fold C ring 25-fold M ring for the basal body of S. Typhimurium.
Sample
  • Sample: Isolated hook-basal body
  • Organelle or cellular component: Basal body
Keywordsbacterial flagellum / Salmonella / C-ring / M-ring / basal body / FliF / FliG
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / negative staining
AuthorsThomas DR / Francis NR / Xu C / DeRosier DJ
CitationJournal: J Bacteriol / Year: 2006
Title: The three-dimensional structure of the flagellar rotor from a clockwise-locked mutant of Salmonella enterica serovar Typhimurium.
Authors: Dennis R Thomas / Noreen R Francis / Chen Xu / David J DeRosier /
Abstract: Three-dimensional reconstructions from electron cryomicrographs of the rotor of the flagellar motor reveal that the symmetry of individual M rings varies from 24-fold to 26-fold while that of the C ...Three-dimensional reconstructions from electron cryomicrographs of the rotor of the flagellar motor reveal that the symmetry of individual M rings varies from 24-fold to 26-fold while that of the C rings, containing the two motor/switch proteins FliM and FliN, varies from 32-fold to 36-fold, with no apparent correlation between the symmetries of the two rings. Results from other studies provided evidence that, in addition to the transmembrane protein FliF, at least some part of the third motor/switch protein, FliG, contributes to a thickening on the face of the M ring, but there was no evidence as to whether or not any portion of FliG also contributes to the C ring. Of the four morphological features in the cross section of the C ring, the feature closest to the M ring is not present with the rotational symmetry of the rest of the C ring, but instead it has the symmetry of the M ring. We suggest that this inner feature arises from a domain of FliG. We present a hypothetical docking in which the C-terminal motor domain of FliG lies in the C ring, where it can interact intimately with FliM.
History
DepositionMar 30, 2011-
Header (metadata) releaseApr 8, 2011-
Map releaseApr 8, 2011-
UpdateApr 8, 2011-
Current statusApr 8, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 68
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 68
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1887.png

Downloads & links

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Map

FileDownload / File: emd_1887.map.gz / Format: CCP4 / Size: 14.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation34-fold C ring 25-fold M ring for the basal body of S. Typhimurium.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.8 Å/pix.
x 120 pix.
= 336. Å		2.8 Å/pix.
x 180 pix.
= 504. Å		2.8 Å/pix.
x 180 pix.
= 504. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 2.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 68.0 / Movie #1: 68
Minimum - Maximum-584.956000000000017 - 575.816000000000031
Average (Standard dev.)2.65061 (±87.968800000000002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180120
Spacing180180120
CellA: 504 Å / B: 504 Å / C: 336 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z180180120
origin x/y/z0.0000.0000.000
length x/y/z504.000504.000336.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180120
D min/max/mean-584.956575.8162.651

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Supplemental data

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Sample components

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Entire : Isolated hook-basal body

EntireName: Isolated hook-basal body
Components
  • Sample: Isolated hook-basal body
  • Organelle or cellular component: Basal body

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Supramolecule #1000: Isolated hook-basal body

SupramoleculeName: Isolated hook-basal body / type: sample / ID: 1000 / Number unique components: 4

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Supramolecule #1: Basal body

SupramoleculeName: Basal body / type: organelle_or_cellular_component / ID: 1 / Name.synonym: Rotor / Details: Frozen-hydrated / Oligomeric state: 34-mer C ring, 25-mer M ring / Recombinant expression: Yes
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
synonym: Salmonella Typhimurium / Location in cell: Plasma membrane and cytoplasm
Recombinant expressionOrganism: Salmonella (bacteria)

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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

BufferpH: 8 / Details: 10mM Tris-HCl, 5 mM EDTA, 0.1% Triton X-100
StainingType: NEGATIVE
Details: Sample put onto Quantifoil grids(R1.2/1.3), blotted with no. 1 Whatman filter paper, plunged into liquid nitrogen-cooled liquid ethane.
GridDetails: Quantifoil grids R1.2/1.3
VitrificationCryogen name: ETHANE / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Home made

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureAverage: 100 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Average electron dose: 10 e/Å2 / Od range: 2 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsThe images were sorted into classes. 20 classes depending on symmetry of M ring (23 to 26) and symmetry of C ring (32 to 36).
CTF correctionDetails: CTFFIND, HELIXBOXER
Final reconstructionSoftware - Name: SPIDER / Number images used: 90

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