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- EMDB-3398: Electron Cryotomography and subvolume averaging of the cytoplasmi... -

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Basic information

Entry
Database: EMDB / ID: EMD-3398
TitleElectron Cryotomography and subvolume averaging of the cytoplasmic chemoreceptor array in Vibrio cholerae
Map datasubvolume average of the cytoplasmic array in V. cholerae
Sample
  • Sample: cytoplasmic array subvolume average from whole cell tomogram
  • Protein or peptide: DosM
Keywordschemotaxis / chemoreceptor / Vibrio cholerae / cytoplasmic chemoreceptor array
Biological speciesVibrio cholerae (bacteria)
Methodsubtomogram averaging / cryo EM
AuthorsBriegel A / Ortega D R / Mann P / Kjaer A / Ringgaard S / Jensen G J
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Chemotaxis cluster 1 proteins form cytoplasmic arrays in Vibrio cholerae and are stabilized by a double signaling domain receptor DosM.
Authors: Ariane Briegel / Davi R Ortega / Petra Mann / Andreas Kjær / Simon Ringgaard / Grant J Jensen /
Abstract: Nearly all motile bacterial cells use a highly sensitive and adaptable sensory system to detect changes in nutrient concentrations in the environment and guide their movements toward attractants and ...Nearly all motile bacterial cells use a highly sensitive and adaptable sensory system to detect changes in nutrient concentrations in the environment and guide their movements toward attractants and away from repellents. The best-studied bacterial chemoreceptor arrays are membrane-bound. Many motile bacteria contain one or more additional, sometimes purely cytoplasmic, chemoreceptor systems. Vibrio cholerae contains three chemotaxis clusters (I, II, and III). Here, using electron cryotomography, we explore V. cholerae's cytoplasmic chemoreceptor array and establish that it is formed by proteins from cluster I. We further identify a chemoreceptor with an unusual domain architecture, DosM, which is essential for formation of the cytoplasmic arrays. DosM contains two signaling domains and spans the two-layered cytoplasmic arrays. Finally, we present evidence suggesting that this type of receptor is important for the structural stability of the cytoplasmic array.
History
DepositionMar 22, 2016-
Header (metadata) releaseMay 4, 2016-
Map releaseAug 31, 2016-
UpdateAug 31, 2016-
Current statusAug 31, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 178
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 178
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

DosMmap.tif

Downloads & links

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Map

FileDownload / File: emd_3398.map.gz / Format: CCP4 / Size: 2.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsubvolume average of the cytoplasmic array in V. cholerae
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.62 Å/pix.
x 101 pix.
= 668.418 Å		6.62 Å/pix.
x 80 pix.
= 529.44 Å		6.62 Å/pix.
x 80 pix.
= 529.44 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: 6.618 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 178.0 / Movie #1: 178
Minimum - Maximum165.449996950000013 - 185.710006709999988
Average (Standard dev.)173.549728390000013 (±2.58399725)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-49
Dimensions8080101
Spacing8080101
CellA: 529.44 Å / B: 529.44 Å / C: 668.418 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.6186.6186.618
M x/y/z8080101
origin x/y/z0.0000.0000.000
length x/y/z529.440529.440668.418
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS00-49
NC/NR/NS8080101
D min/max/mean165.450185.710173.550

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Supplemental data

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Sample components

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Entire : cytoplasmic array subvolume average from whole cell tomogram

EntireName: cytoplasmic array subvolume average from whole cell tomogram
Components
  • Sample: cytoplasmic array subvolume average from whole cell tomogram
  • Protein or peptide: DosM

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Supramolecule #1000: cytoplasmic array subvolume average from whole cell tomogram

SupramoleculeName: cytoplasmic array subvolume average from whole cell tomogram
type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: DosM

MacromoleculeName: DosM / type: protein_or_peptide / ID: 1 / Oligomeric state: Dimer / Recombinant expression: No
Source (natural)Organism: Vibrio cholerae (bacteria) / Location in cell: cytoplasm

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

GridDetails: Quantifoil R2/2 copper grids, glow discharged
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: Gatan / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateJun 4, 2015
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 121 / Average electron dose: 160 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal magnification: 33000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Software - Name: imod / Number subtomograms used: 80
CTF correctionDetails: imod

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