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- EMDB-10160: In Situ Core-Signalling Unit of E. coli Chemoreceptor Array -

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Basic information

Entry
Database: EMDB / ID: EMD-10160
TitleIn Situ Core-Signalling Unit of E. coli Chemoreceptor Array
Map dataNone
Sample
  • Cell: Optimised E. coli minicell strain WM4196 containing native-state chemoreceptor arrays.
Biological speciesEscherichia coli (E. coli)
Methodsubtomogram averaging / cryo EM / Resolution: 16.0 Å
AuthorsBurt A / Desfosses A / Gutsche I
Funding support1 items
OrganizationGrant numberCountry
European Research Council647784
CitationJournal: Nat Commun / Year: 2020
Title: Complete structure of the chemosensory array core signalling unit in an E. coli minicell strain.
Authors: Alister Burt / C Keith Cassidy / Peter Ames / Maria Bacia-Verloop / Megghane Baulard / Karine Huard / Zaida Luthey-Schulten / Ambroise Desfosses / Phillip J Stansfeld / William Margolin / ...Authors: Alister Burt / C Keith Cassidy / Peter Ames / Maria Bacia-Verloop / Megghane Baulard / Karine Huard / Zaida Luthey-Schulten / Ambroise Desfosses / Phillip J Stansfeld / William Margolin / John S Parkinson / Irina Gutsche /
Abstract: Motile bacteria sense chemical gradients with transmembrane receptors organised in supramolecular signalling arrays. Understanding stimulus detection and transmission at the molecular level requires ...Motile bacteria sense chemical gradients with transmembrane receptors organised in supramolecular signalling arrays. Understanding stimulus detection and transmission at the molecular level requires precise structural characterisation of the array building block known as a core signalling unit. Here we introduce an Escherichia coli strain that forms small minicells possessing extended and highly ordered chemosensory arrays. We use cryo-electron tomography and subtomogram averaging to provide a three-dimensional map of a complete core signalling unit, with visible densities corresponding to the HAMP and periplasmic domains. This map, combined with previously determined high resolution structures and molecular dynamics simulations, yields a molecular model of the transmembrane core signalling unit and enables spatial localisation of its individual domains. Our work thus offers a solid structural basis for the interpretation of a wide range of existing data and the design of further experiments to elucidate signalling mechanisms within the core signalling unit and larger array.
History
DepositionJul 30, 2019-
Header (metadata) releaseAug 7, 2019-
Map releaseAug 7, 2019-
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: 0.0144
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0144
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10160.png

Downloads & links

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Map

FileDownload / File: emd_10160.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 4.48 Å
Density
Contour LevelBy AUTHOR: 0.0144 / Movie #1: 0.0144
Minimum - Maximum-0.04888741 - 0.09695427
Average (Standard dev.)0.0002669176 (±0.010366776)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 573.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.484.484.48
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z573.440573.440573.440
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0490.0970.000

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Supplemental data

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Mask #1

Fileemd_10160_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Mask #2

Fileemd_10160_msk_2.map
Projections & Slices
AxesZYX

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Additional map: Local resolution filtered map centered on 3fold axis...

Fileemd_10160_additional.map
AnnotationLocal resolution filtered map centered on 3fold axis of chemoreceptor array.
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Local resolution filtered map centered on 3fold axis...

Fileemd_10160_additional_1.map
AnnotationLocal resolution filtered map centered on 3fold axis of chemoreceptor array.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: even half map.

Fileemd_10160_half_map_1.map
Annotationeven half map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: odd half map.

Fileemd_10160_half_map_2.map
Annotationodd half map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Optimised E. coli minicell strain WM4196 containing native-state ...

EntireName: Optimised E. coli minicell strain WM4196 containing native-state chemoreceptor arrays.
Components
  • Cell: Optimised E. coli minicell strain WM4196 containing native-state chemoreceptor arrays.

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Supramolecule #1: Optimised E. coli minicell strain WM4196 containing native-state ...

SupramoleculeName: Optimised E. coli minicell strain WM4196 containing native-state chemoreceptor arrays.
type: cell / ID: 1 / Parent: 0
Details: Minicells isolated from WM4196 cell culture by differential centrifugation.
Source (natural)Organism: Escherichia coli (E. coli) / Strain: WM4196

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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
GridModel: Quantifoil R3.5/1 / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: 25 mA
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus min: 0.0002 µm
Specialist opticsPhase plate: VOLTA PHASE PLATE
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-5 / Number grids imaged: 1 / Average electron dose: 1.0 e/Å2
Details: Images were collected in movie mode, 5 frames per movie.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 4 / Number images used: 618 / Software - Name: Dynamo
Final angle assignmentType: NOT APPLICABLE / Software - Name: Dynamo
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo
Details: C3 symmetry applied during refinement. Masks used containing varying extents of the array and the inner membrane were used.
Number subtomograms used: 618
FSC plot (resolution estimation)

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