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- EMDB-0465: Pseudomonas aeruginosa bacterial flagellar motor -

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Basic information

Database: EMDB / ID: EMD-0465
TitlePseudomonas aeruginosa bacterial flagellar motor
Map data
SamplePseudomonas aeruginosa (bacteria)
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 59 Å
AuthorsKaplan M / Ghosal D / Subramanian P / Oikonomou CO / Kjaer A / Pirbadian S / Ortega DR / Briegel A / El-Naggar MY / Jensen GJ
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
DepositionJan 15, 2019-
Header (metadata) releaseJan 30, 2019-
Map releaseJan 30, 2019-
UpdateJan 30, 2019-
Current statusJan 30, 2019Processing site: RCSB / Status: Released

Structure visualization

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

Downloads & links


FileDownload / File: emd_0465.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
13.06 Å/pix.
x 70 pix.
= 914.2 Å
13.06 Å/pix.
x 100 pix.
= 1306. Å
13.06 Å/pix.
x 70 pix.
= 914.2 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 13.06 Å
Contour LevelBy AUTHOR: 179.0 / Movie #1: 179
Minimum - Maximum0.0 - 255.0
Average (Standard dev.)141.957439999999991 (±43.699986000000003)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA: 914.2 Å / B: 1306.0 Å / C: 914.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z13.0613.0613.06
M x/y/z7010070
origin x/y/z0.0000.0000.000
length x/y/z914.2001306.000914.200
MAP C/R/S123
start NC/NR/NS000
D min/max/mean0.000255.000141.957

Supplemental data

Sample components

Entire Pseudomonas aeruginosa

EntireName: Pseudomonas aeruginosa (bacteria) / Number of components: 1

Component #1: cellular-component, Pseudomonas aeruginosa

Cellular-componentName: Pseudomonas aeruginosa / Recombinant expression: No
SourceSpecies: Pseudomonas aeruginosa (bacteria)

Experimental details

Sample preparation

SpecimenSpecimen state: Cell / Method: cryo EM
Sample solutionpH: 7
VitrificationCryogen name: OTHER

Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C2 (2 fold cyclic) / Number of subtomograms: 144
3D reconstructionResolution: 59 Å / Resolution method: FSC 0.143 CUT-OFF

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