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Yorodumi- EMDB-14396: Tomogram of wild-type mouse neuronal growth cone (T-zone), 4 x bi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14396 | |||||||||||||||||||||
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Title | Tomogram of wild-type mouse neuronal growth cone (T-zone), 4 x binned, processed. | |||||||||||||||||||||
Map data | Tomogram of wild-type mouse neuronal growth cone (T-zone), 4 x binned, processed. | |||||||||||||||||||||
Sample |
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Keywords | Growth Cone / Neurons / Actin / Microtubules / Tomogram / CELL INVASION | |||||||||||||||||||||
Biological species | Mus (mice) | |||||||||||||||||||||
Method | electron tomography / cryo EM | |||||||||||||||||||||
Authors | Atherton J / Stouffer M / Francis F / Moores CA | |||||||||||||||||||||
Funding support | United Kingdom, France, 6 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14396.map.gz | 608.5 MB | EMDB map data format | |
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Header (meta data) | emd-14396-v30.xml emd-14396.xml | 9.2 KB 9.2 KB | Display Display | EMDB header |
Images | emd_14396.png | 259.3 KB | ||
Filedesc metadata | emd-14396.cif.gz | 4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14396 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14396 | HTTPS FTP |
-Validation report
Summary document | emd_14396_validation.pdf.gz | 383.2 KB | Display | EMDB validaton report |
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Full document | emd_14396_full_validation.pdf.gz | 382.7 KB | Display | |
Data in XML | emd_14396_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | emd_14396_validation.cif.gz | 5.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14396 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14396 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_14396.map.gz / Format: CCP4 / Size: 655.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||
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Annotation | Tomogram of wild-type mouse neuronal growth cone (T-zone), 4 x binned, processed. | ||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 21.55 Å | ||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Tomogram of wild-type mouse neuronal growth cone (T-zone), 4 x bi...
Entire | Name: Tomogram of wild-type mouse neuronal growth cone (T-zone), 4 x binned, processed. |
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Components |
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-Supramolecule #1: Tomogram of wild-type mouse neuronal growth cone (T-zone), 4 x bi...
Supramolecule | Name: Tomogram of wild-type mouse neuronal growth cone (T-zone), 4 x binned, processed. type: cell / ID: 1 / Parent: 0 / Details: In situ tomogram |
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Source (natural) | Organism: Mus (mice) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 / Details: Cells were cultured in neurobasal media |
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Grid | Model: Quantifoil R2/4 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE |
Details | In situ tomogram |
Sectioning | Other: NO SECTIONING |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 110.0 e/Å2 / Details: Dose weighted |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: IMOD Details: Tomogram binned x 4 and B-factor of 100,000 applied for display. Number images used: 41 |
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