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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: EMD-8603
TitleSub-tomogram average of the archaellar motor in Thermococcus kodakaraensis
Map data
Sample
  • Complex: Archaellar motor
Biological speciesThermococcus kodakaraensis (archaea)
Methodsubtomogram averaging / cryo EM / Resolution: 40.0 Å
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 ...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.
History
DepositionFeb 13, 2017-
Header (metadata) releaseFeb 22, 2017-
Map releaseJul 26, 2017-
UpdateFeb 14, 2018-
Current statusFeb 14, 2018Processing site: RCSB / Status: Released

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Structure visualization

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

emd_8603.png

Downloads & links

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Map

FileDownload / File: emd_8603.map.gz / Format: CCP4 / Size: 977.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.067 / Movie #1: 0.067
Minimum - Maximum0.012801021 - 0.1403
Average (Standard dev.)0.05666378 (±0.01550041)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions1005050
Spacing5010050
CellA: 330.0 Å / B: 660.0 Å / C: 330.0 Å
α=β=γ: 90.0 °

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
Components
  • Complex: Archaellar motor

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Supramolecule #1: Archaellar motor

SupramoleculeName: Archaellar motor / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Thermococcus kodakaraensis (archaea)

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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: 7
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: 1.5 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: C20 (20 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 40.0 Å / Resolution method: OTHER / Software - Name: TOMO3D / Number subtomograms used: 30
ExtractionNumber tomograms: 9 / Number images used: 30 / Software - Name: PEET
CTF correctionSoftware - Name: IMOD
Final 3D classificationSoftware - Name: PEET
Final angle assignmentType: OTHER / Software - Name: PEET

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