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- EMDB-3911: Bdellovibrio bacteriovorus bacterial flagellar motor -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-3911
TitleBdellovibrio bacteriovorus bacterial flagellar motor
Map dataBdellovibrio bacteriovorus bacterial flagellar motor
Sample
  • Complex: Bdellovibrio bacteriovorus flagellar motor
Biological speciesBdellovibrio bacteriovorus (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 82.0 Å
AuthorsChaban B / Coleman I / Beeby M
CitationJournal: Sci Rep / Year: 2018
Title: Evolution of higher torque in Campylobacter-type bacterial flagellar motors.
Authors: Bonnie Chaban / Izaak Coleman / Morgan Beeby /
Abstract: Understanding the evolution of molecular machines underpins our understanding of the development of life on earth. A well-studied case are bacterial flagellar motors that spin helical propellers for ...Understanding the evolution of molecular machines underpins our understanding of the development of life on earth. A well-studied case are bacterial flagellar motors that spin helical propellers for bacterial motility. Diverse motors produce different torques, but how this diversity evolved remains unknown. To gain insights into evolution of the high-torque ε-proteobacterial motor exemplified by the Campylobacter jejuni motor, we inferred ancestral states by combining phylogenetics, electron cryotomography, and motility assays to characterize motors from Wolinella succinogenes, Arcobacter butzleri and Bdellovibrio bacteriovorus. Observation of ~12 stator complexes in many proteobacteria, yet ~17 in ε-proteobacteria suggest a "quantum leap" evolutionary event. Campylobacter-type motors have high stator occupancy in wider rings of additional stator complexes that are scaffolded by large proteinaceous periplasmic rings. We propose a model for motor evolution wherein independent inner- and outer-membrane structures fused to form a scaffold for additional stator complexes. Significantly, inner- and outer-membrane associated structures have evolved independently multiple times, suggesting that evolution of such structures is facile and poised the ε-proteobacteria to fuse them to form the high-torque Campylobacter-type motor.
History
DepositionOct 11, 2017-
Header (metadata) releaseDec 20, 2017-
Map releaseJan 17, 2018-
UpdateJan 17, 2018-
Current statusJan 17, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3911.png

Downloads & links

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Map

FileDownload / File: emd_3911.map.gz / Format: CCP4 / Size: 24.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBdellovibrio bacteriovorus bacterial flagellar motor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.12 Å/pix.
x 186 pix.
= 1510.692 Å		8.12 Å/pix.
x 186 pix.
= 1510.692 Å		8.12 Å/pix.
x 186 pix.
= 1510.692 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.122 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.2
Minimum - Maximum-0.62034863 - 0.88331884
Average (Standard dev.)0.007004884 (±0.061880827)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions186186186
Spacing186186186
CellA=B=C: 1510.6919 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z8.1228.1228.122
M x/y/z186186186
origin x/y/z0.0000.0000.000
length x/y/z1510.6921510.6921510.692
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS186186186
D min/max/mean-0.6200.8830.007

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Supplemental data

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Sample components

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Entire : Bdellovibrio bacteriovorus flagellar motor

EntireName: Bdellovibrio bacteriovorus flagellar motor
Components
  • Complex: Bdellovibrio bacteriovorus flagellar motor

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Supramolecule #1: Bdellovibrio bacteriovorus flagellar motor

SupramoleculeName: Bdellovibrio bacteriovorus flagellar motor / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bdellovibrio bacteriovorus (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/2
VitrificationCryogen name: ETHANE-PROPANE
DetailsIn situ

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Electron microscopy

MicroscopeFEI TECNAI 20
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 82.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET / Number subtomograms used: 478
ExtractionNumber tomograms: 478 / Number images used: 478
Final angle assignmentType: NOT APPLICABLE

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