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- EMDB-11385: Treponema denticola chemotaxis signalling arrays -

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Basic information

Entry
Database: EMDB / ID: EMD-11385
TitleTreponema denticola chemotaxis signalling arrays
Map dataTreponema denticola chemotaxis arrays
Sample
  • Cell: Chemotaxis arrays in a Treponema denticola ODP (TDE2498) deletion mutant
Biological speciesTreponema denticola (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 16.0 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

Movie
  • Surface view with section colored by density value
  • Surface level: 0.946
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.946
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

emd_11385.png

Downloads & links

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Map

FileDownload / File: emd_11385.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTreponema denticola chemotaxis arrays
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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 7.026 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.946 / Movie #1: 0.946
Minimum - Maximum-3.7606003 - 4.2879
Average (Standard dev.)0.52727145 (±0.105238184)
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-3.7614.2880.527

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Supplemental data

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Mask #1

Fileemd_11385_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Half map: Half map 2

Fileemd_11385_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Half map: Half map 1

Fileemd_11385_half_map_2.map
AnnotationHalf map 1
Projections & Slices
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Histogram

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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
Components
  • Cell: Chemotaxis arrays in a Treponema denticola ODP (TDE2498) deletion mutant

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Supramolecule #1: Chemotaxis arrays in a Treponema denticola ODP (TDE2498) deletion...

SupramoleculeName: Chemotaxis arrays in a Treponema denticola ODP (TDE2498) deletion mutant
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Treponema denticola (bacteria)

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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: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 20 K / Instrument: LEICA PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.33 CUT-OFF / Number subtomograms used: 728
ExtractionNumber tomograms: 10 / Number images used: 728
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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