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- EMDB-0464: Legionella pneumophila bacterial flagellar motor -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-0464
TitleLegionella pneumophila bacterial flagellar motor
Map dataem-volume_P1
Sample
  • Complex: Legionella pneumophila bacterial flagellar motor
Biological speciesLegionella pneumophila (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 64.0 Å
AuthorsKaplan M / Ghosal D / Subramanian P / Oikonomou CO / Kjaer A / Pirbadian S / Ortega DR / Briegel A / El-Naggar MY / Jensen GJ
Citation
Journal: Elife / Year: 2019
Title: The presence and absence of periplasmic rings in bacterial flagellar motors correlates with stator type.
Authors: Mohammed Kaplan / Debnath Ghosal / Poorna Subramanian / Catherine M Oikonomou / Andreas Kjaer / Sahand Pirbadian / Davi R Ortega / Ariane Briegel / Mohamed Y El-Naggar / Grant J Jensen /
Abstract: The bacterial flagellar motor, a cell-envelope-embedded macromolecular machine that functions as a cellular propeller, exhibits significant structural variability between species. Different torque- ...The bacterial flagellar motor, a cell-envelope-embedded macromolecular machine that functions as a cellular propeller, exhibits significant structural variability between species. Different torque-generating stator modules allow motors to operate in different pH, salt or viscosity levels. How such diversity evolved is unknown. Here, we use electron cryo-tomography to determine the in situ macromolecular structures of three Gammaproteobacteria motors: , , and , providing the first views of intact motors with dual stator systems. Complementing our imaging with bioinformatics analysis, we find a correlation between the motor's stator system and its structural elaboration. Motors with a single H-driven stator have only the core periplasmic P- and L-rings; those with dual H-driven stators have an elaborated P-ring; and motors with Na or Na/H-driven stators have both their P- and L-rings embellished. Our results suggest an evolution of structural elaboration that may have enabled pathogenic bacteria to colonize higher-viscosity environments in animal hosts.
#1: Journal: bioRxiv
Title: The structural complexity of the Gammaproteobacteria flagellar motor is related to the type of its torque-generating stators
Authors: Kaplan M / Ghosal D / Subramanian P / Oikonomou CO / Kjaer A / Pirbadian S / Ortega DR / El-Naggar MY / Jensen GJ
History
DepositionJan 15, 2019-
Header (metadata) releaseJan 30, 2019-
Map releaseJan 30, 2019-
UpdateJan 30, 2019-
Current statusJan 30, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 179
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 179
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0464.png

Downloads & links

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Map

FileDownload / File: emd_0464.map.gz / Format: CCP4 / Size: 684.6 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationem-volume_P1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
15.6 Å/pix.
x 50 pix.
= 780. Å		15.6 Å/pix.
x 70 pix.
= 1092. Å		15.6 Å/pix.
x 50 pix.
= 780. 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: 15.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 179.0 / Movie #1: 179
Minimum - Maximum0.0 - 255.0
Average (Standard dev.)134.840480000000014 (±49.389496000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions705050
Spacing507050
CellA: 780.0 Å / B: 1092.0 Å / C: 780.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z15.615.615.6
M x/y/z507050
origin x/y/z0.0000.0000.000
length x/y/z780.0001092.000780.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS507050
D min/max/mean0.000255.000134.840

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Supplemental data

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Sample components

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Entire : Legionella pneumophila bacterial flagellar motor

EntireName: Legionella pneumophila bacterial flagellar motor
Components
  • Complex: Legionella pneumophila bacterial flagellar motor

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Supramolecule #1: Legionella pneumophila bacterial flagellar motor

SupramoleculeName: Legionella pneumophila bacterial flagellar motor / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Legionella pneumophila (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 6.9
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 64.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: IMOD, TOMO3D, PEET) / Number subtomograms used: 44
ExtractionNumber tomograms: 50 / Number images used: 44
Final angle assignmentType: OTHER

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