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- EMDB-2610: Electron tomography of zipping in Drosophyla melanogaster -

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Basic information

Entry
Database: EMDB / ID: EMD-2610
TitleElectron tomography of zipping in Drosophyla melanogaster
Map dataTomographic reconstruction of Drosophila zipping
Sample
  • Sample: Tomographic reconstruction of an entire zipping in Drosophila embryo
  • Organelle or cellular component: zipping in Drosphila embryogenesis
Keywordsepithelial tissue sealing / dorsal closure / serial tomography / high pressure freezing / freeze-substitution
Biological speciesDrosophila melanogaster (fruit fly)
Methodelectron tomography / cryo EM / negative staining
AuthorsEltsov M / Dube N / Yu Z / Haselmann-Weiss U / Brunner D / Frangakis A S
CitationJournal: Nat Cell Biol / Year: 2015
Title: Quantitative analysis of cytoskeletal reorganization during epithelial tissue sealing by large-volume electron tomography.
Authors: Mikhail Eltsov / Nadia Dubé / Zhou Yu / Laurynas Pasakarnis / Uta Haselmann-Weiss / Damian Brunner / Achilleas S Frangakis /
Abstract: The closure of epidermal openings is an essential biological process that causes major developmental problems such as spina bifida in humans if it goes awry. At present, the mechanism of closure ...The closure of epidermal openings is an essential biological process that causes major developmental problems such as spina bifida in humans if it goes awry. At present, the mechanism of closure remains elusive. Therefore, we reconstructed a model closure event, dorsal closure in fly embryos, by large-volume correlative electron tomography. We present a comprehensive, quantitative analysis of the cytoskeletal reorganization, enabling separated epidermal cells to seal the epithelium. After establishing contact through actin-driven exploratory filopodia, cells use a single lamella to generate 'roof tile'-like overlaps. These shorten to produce the force, 'zipping' the tissue closed. The shortening overlaps lack detectable actin filament ensembles but are crowded with microtubules. Cortical accumulation of shrinking microtubule ends suggests a force generation mechanism in which cortical motors pull on microtubule ends as for mitotic spindle positioning. In addition, microtubules orient filopodia and lamellae before zipping. Our 4D electron microscopy picture describes an entire developmental process and provides fundamental insight into epidermal closure.
History
DepositionMar 21, 2014-
Header (metadata) releaseApr 30, 2014-
Map releaseApr 15, 2015-
UpdateMay 13, 2015-
Current statusMay 13, 2015Processing site: PDBe / Status: Released

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Structure visualization

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Supplemental images

emd_2610.tif

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Map

FileDownload / File: emd_2610.map.gz / Format: CCP4 / Size: 1 GB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationTomographic reconstruction of Drosophila zipping
Voxel sizeX: 59 Å / Y: 59 Å / Z: 81 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)1.30015326 (±30.184339520000002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin957-5214
Dimensions9998921254
Spacing9998921254
CellA: 52628.0 Å / B: 58941.0 Å / C: 101574.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z595981
M x/y/z8929991254
origin x/y/z0.0000.0000.000
length x/y/z52628.00058941.000101574.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-5295714
NC/NR/NS8929991254
D min/max/mean-128.000127.0001.300

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Supplemental data

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Sample components

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Entire : Tomographic reconstruction of an entire zipping in Drosophila embryo

EntireName: Tomographic reconstruction of an entire zipping in Drosophila embryo
Components
  • Sample: Tomographic reconstruction of an entire zipping in Drosophila embryo
  • Organelle or cellular component: zipping in Drosphila embryogenesis

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Supramolecule #1000: Tomographic reconstruction of an entire zipping in Drosophila embryo

SupramoleculeName: Tomographic reconstruction of an entire zipping in Drosophila embryo
type: sample / ID: 1000
Details: Joined 34 serial tomograms were reconstructed from 2x2 montaged tilt-series. Tilt-series were recorded at x12000 corresponding to 0.9nm/pixel at the specimen level. The map was binned for ...Details: Joined 34 serial tomograms were reconstructed from 2x2 montaged tilt-series. Tilt-series were recorded at x12000 corresponding to 0.9nm/pixel at the specimen level. The map was binned for deposition to reduce the file size. The z-axis of the map corresponds to the anterior/posterior embryonic axis while the y-axis to the ventral/dorsal axis. The dorsal epidermal cells are located on the top.
Number unique components: 1

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Supramolecule #1: zipping in Drosphila embryogenesis

SupramoleculeName: zipping in Drosphila embryogenesis / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: fruit fly

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingelectron tomography
Aggregation statetissue

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Sample preparation

StainingType: NEGATIVE
Details: Sections were stained with 2% UA in 70% methanol and Reynolds lead citrate.
GridDetails: slot grids with Formvar support
VitrificationCryogen name: NITROGEN / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 12000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° / Tilt series - Axis1 - Angle increment: 1.5 °
DateMay 10, 2010
Image recordingCategory: FILM / Film or detector model: FEI EAGLE (4k x 4k) / Digitization - Scanner: OTHER
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: ETOMO / Number images used: 120

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