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- EMDB-14401: Tomogram of doublecortin knock-out mouse neuronal growth cone (C-... -

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Basic information

Entry
Database: EMDB / ID: EMD-14401
TitleTomogram of doublecortin knock-out mouse neuronal growth cone (C-zone), 4 x binned, processed.
Map dataTomogram of doublecortin knock-out mouse neuronal growth cone (C-zone), 4 x binned, processed.
Sample
  • Cell: Tomogram of doublecortin knock-out mouse neuronal growth cone (C-zone), 4 x binned, processed.
KeywordsGrowth Cone / Neurons / Actin / Microtubules / Tomogram / CELL INVASION
Biological speciesMus (mice)
Methodelectron tomography / cryo EM
AuthorsAtherton J / Stouffer M / Francis F / Moores CA
Funding support United Kingdom, France, 6 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/R000352/1 United Kingdom
Wellcome Trust079605/Z/06/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L014211/1 United Kingdom
Agence Nationale de la Recherche (ANR)ANR-16-CE16-0011-03 France
Other governmentEU-HEALTH-2013, DESIRE, Number 60253
Other governmentCOST Action CA16118
CitationJournal: J Cell Sci / Year: 2022
Title: Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography.
Authors: Joseph Atherton / Melissa Stouffer / Fiona Francis / Carolyn A Moores /
Abstract: Neurons extend axons to form the complex circuitry of the mature brain. This depends on the coordinated response and continuous remodelling of the microtubule and F-actin networks in the axonal ...Neurons extend axons to form the complex circuitry of the mature brain. This depends on the coordinated response and continuous remodelling of the microtubule and F-actin networks in the axonal growth cone. Growth cone architecture remains poorly understood at nanoscales. We therefore investigated mouse hippocampal neuron growth cones using cryo-electron tomography to directly visualise their three-dimensional subcellular architecture with molecular detail. Our data showed that the hexagonal arrays of actin bundles that form filopodia penetrate and terminate deep within the growth cone interior. We directly observed the modulation of these and other growth cone actin bundles by alteration of individual F-actin helical structures. Microtubules with blunt, slightly flared or gently curved ends predominated in the growth cone, frequently contained lumenal particles and exhibited lattice defects. Investigation of the effect of absence of doublecortin, a neurodevelopmental cytoskeleton regulator, on growth cone cytoskeleton showed no major anomalies in overall growth cone organisation or in F-actin subpopulations. However, our data suggested that microtubules sustained more structural defects, highlighting the importance of microtubule integrity during growth cone migration.
History
DepositionFeb 21, 2022-
Header (metadata) releaseApr 20, 2022-
Map releaseApr 20, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14401.png

Downloads & links

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Map

FileDownload / File: emd_14401.map.gz / Format: CCP4 / Size: 655.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomogram of doublecortin knock-out mouse neuronal growth cone (C-zone), 4 x binned, processed.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
21.55 Å/pix.
x 200 pix.
= 4310. Å		21.55 Å/pix.
x 927 pix.
= 19976.85 Å		21.55 Å/pix.
x 927 pix.
= 19976.85 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 21.55 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-16.452805000000001 - 15.455895999999999
Average (Standard dev.)-0.0029290544 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-214748364800
Dimensions927927200
Spacing927927200
CellA: 19976.85 Å / B: 19976.85 Å / C: 4310.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Tomogram of doublecortin knock-out mouse neuronal growth cone (C-...

EntireName: Tomogram of doublecortin knock-out mouse neuronal growth cone (C-zone), 4 x binned, processed.
Components
  • Cell: Tomogram of doublecortin knock-out mouse neuronal growth cone (C-zone), 4 x binned, processed.

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Supramolecule #1: Tomogram of doublecortin knock-out mouse neuronal growth cone (C-...

SupramoleculeName: Tomogram of doublecortin knock-out mouse neuronal growth cone (C-zone), 4 x binned, processed.
type: cell / ID: 1 / Parent: 0 / Details: In situ tomogram
Source (natural)Organism: Mus (mice)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7 / Details: Cells were cultured in neurobasal media
GridModel: Quantifoil R2/4 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE
DetailsIn situ tomogram
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 110.0 e/Å2 / Details: Dose weighted
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 41

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