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- EMDB-11381: Treponema denticola chemotaxis signalling arrays in an ODP (TDE24... -

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Basic information

Entry
Database: EMDB / ID: EMD-11381
TitleTreponema denticola chemotaxis signalling arrays in an ODP (TDE2498) deletion mutant
Map data
SampleChemotaxis arrays in a Treponema denticola ODP (TDE2498) deletion mutant
Biological speciesTreponema denticola (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 28.2 Å
AuthorsMuok AR / Yang W / Briegel A
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)184.034.014 Netherlands
CitationJournal: Nat Commun / Year: 2020
Title: Atypical chemoreceptor arrays accommodate high membrane curvature.
Authors: Alise R Muok / Davi R Ortega / Kurni Kurniyati / Wen Yang / Zachary A Maschmann / Adam Sidi Mabrouk / Chunhao Li / Brian R Crane / Ariane Briegel /
Abstract: The prokaryotic chemotaxis system is arguably the best-understood signaling pathway in biology. In all previously described species, chemoreceptors organize into a hexagonal (P6 symmetry) extended ...The prokaryotic chemotaxis system is arguably the best-understood signaling pathway in biology. In all previously described species, chemoreceptors organize into a hexagonal (P6 symmetry) extended array. Here, we report an alternative symmetry (P2) of the chemotaxis apparatus that emerges from a strict linear organization of the histidine kinase CheA in Treponema denticola cells, which possesses arrays with the highest native curvature investigated thus far. Using cryo-ET, we reveal that Td chemoreceptor arrays assume an unusual arrangement of the supra-molecular protein assembly that has likely evolved to accommodate the high membrane curvature. The arrays have several atypical features, such as an extended dimerization domain of CheA and a variant CheW-CheR-like fusion protein that is critical for maintaining an ordered chemosensory apparatus. Furthermore, the previously characterized Td oxygen sensor ODP influences CheA ordering. These results suggest a greater diversity of the chemotaxis signaling system than previously thought.
History
DepositionJul 14, 2020-
Header (metadata) releaseOct 28, 2020-
Map releaseOct 28, 2020-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

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  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Map

FileDownload / File: emd_11381.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.03 Å/pix.
x 128 pix.
= 899.328 Å
7.03 Å/pix.
x 128 pix.
= 899.328 Å
7.03 Å/pix.
x 128 pix.
= 899.328 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.026 Å
Density
Contour LevelBy AUTHOR: 1.4 / Movie #1: 0.4
Minimum - Maximum-4.0659 - 4.0659
Average (Standard dev.)-0.097993866 (±0.11635313)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 899.328 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.0267.0267.026
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z899.328899.328899.328
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ172172172
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-4.0664.066-0.098

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Supplemental data

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Sample components

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Entire Chemotaxis arrays in a Treponema denticola ODP (TDE2498) deletion...

EntireName: Chemotaxis arrays in a Treponema denticola ODP (TDE2498) deletion mutant
Number of components: 1

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Component #1: cellular-component, Chemotaxis arrays in a Treponema denticola OD...

Cellular-componentName: Chemotaxis arrays in a Treponema denticola ODP (TDE2498) deletion mutant
Recombinant expression: No
SourceSpecies: Treponema denticola (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Cell / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: LEICA PLUNGER / Cryogen name: ETHANE / Temperature: 20 K / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.6 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric) / Number of subtomograms: 894
3D reconstructionResolution: 28.2 Å / Resolution method: FSC 0.33 CUT-OFF
FSC plot (resolution estimation)

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