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- EMDB-8603: Sub-tomogram average of the archaellar motor in Thermococcus koda... -

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Basic information

Entry
Database: EMDB / ID: 8603
TitleSub-tomogram average of the archaellar motor in Thermococcus kodakaraensis
Map data
SampleArchaellar motor:
SourceThermococcus kodakaraensis (archaea)
Methodsubtomogram averaging / cryo EM / 40 Å resolution
AuthorsChang Y-W / Kjaer A / Briegel A / Oikonomou CM / Jensen GJ
CitationJournal: EMBO Rep. / Year: 2017
Title: Morphology of the archaellar motor and associated cytoplasmic cone in .
Authors: Ariane Briegel / Catherine M Oikonomou / Yi-Wei Chang / Andreas Kjær / Audrey N Huang / Ki Woo Kim / Debnath Ghosal / Hong H Nguyen / Dorothy Kenny / Rachel R Ogorzalek Loo / Robert P Gunsalus / Grant J Jensen
Abstract: Archaeal swimming motility is driven by archaella: rotary motors attached to long extracellular filaments. The structure of these motors, and particularly how they are anchored in the absence of a ...Archaeal swimming motility is driven by archaella: rotary motors attached to long extracellular filaments. The structure of these motors, and particularly how they are anchored in the absence of a peptidoglycan cell wall, is unknown. Here, we use electron cryotomography to visualize the archaellar basal body in KOD1. Compared to the homologous bacterial type IV pilus (T4P), we observe structural similarities as well as several unique features. While the position of the cytoplasmic ATPase appears conserved, it is not braced by linkages that extend upward through the cell envelope as in the T4P, but rather by cytoplasmic components that attach it to a large conical frustum up to 500 nm in diameter at its base. In addition to anchoring the lophotrichous bundle of archaella, the conical frustum associates with chemosensory arrays and ribosome-excluding material and may function as a polar organizing center for the coccoid cells.
DateDeposition: Feb 13, 2017 / Header (metadata) release: Feb 22, 2017 / Map release: Jul 26, 2017 / Last update: Feb 14, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.067
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.067
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

Fileemd_8603.map.gz (map file in CCP4 format, 1001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
50 pix
6.6 Å/pix.
= 330. Å
100 pix
6.6 Å/pix.
= 660. Å
50 pix
6.6 Å/pix.
= 330. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.6 Å
Density
Contour Level:0.067 (by author), 0.067 (movie #1):
Minimum - Maximum0.012801021 - 0.1403
Average (Standard dev.)0.05666378 (0.01550041)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions1005050
Origin000
Limit994949
Spacing5010050
CellA: 330 Å / B: 660 Å / C: 330 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.66.66.6
M x/y/z5010050
origin x/y/z0.0000.0000.000
length x/y/z330.000660.000330.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS5010050
D min/max/mean0.0130.1400.057

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Supplemental data

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Sample components

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Entire Archaellar motor

EntireName: Archaellar motor / Number of components: 1

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Component #1: protein, Archaellar motor

ProteinName: Archaellar motor / Recombinant expression: No
SourceSpecies: Thermococcus kodakaraensis (archaea)

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Experimental details

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Sample preparation

SpecimenSpecimen state: cell / Method: cryo EM
Sample solutionpH: 7
VitrificationCryogen name: ETHANE-PROPANE MIXTURE

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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: 1.5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C20 (20 fold cyclic)
3D reconstructionSoftware: TOMO3D / Resolution: 40 Å / Resolution method: OTHER

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