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- EMDB-53238: Invasive protrusion of a flam-del-412-St2 Drosophila follicle -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-53238
TitleInvasive protrusion of a flam-del-412-St2 Drosophila follicle
Map datadual axis tomogram of a 250nm thick section of epon embedded ovaries from Drosophila flam-del-412-St2;iso-1 genotype
Sample
  • Tissue: Drosophila flam-del-412-St2;iso-1 ovary
KeywordsTransposable elements / retroviruses / membranes / oogenesis / VIRUS LIKE PARTICLE
Biological speciesDrosophila melanogaster (fruit fly)
Methodelectron tomography / cryo EM / negative staining
AuthorsVoichek M / Bernhard A / Brennecke J
Funding supportEuropean Union, Austria, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Austrian Science Fund Austria
CitationJournal: BioRxiv
Title: Direct cell-to-cell transmission of retrotransposons
Authors: Voichek M / Bernhard A / Novatchkova M / Handle D / Moeseneder P / Rafanel B / Duchek P / Senti KA / Brennecke J
History
DepositionMar 24, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53238.png

Downloads & links

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Map

FileDownload / File: emd_53238.map.gz / Format: CCP4 / Size: 5.7 GB / Type: IMAGE STORED AS SIGNED BYTE
Annotationdual axis tomogram of a 250nm thick section of epon embedded ovaries from Drosophila flam-del-412-St2;iso-1 genotype
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.67 Å/pix.
x 472 pix.
= 2675.296 Å		5.67 Å/pix.
x 3340 pix.
= 18931.121 Å		5.67 Å/pix.
x 3868 pix.
= 21923.824 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: 5.668 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)5.8495083 (±32.977229999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-212-164242
Dimensions33403868472
Spacing38683340472
CellA: 21923.824 Å / B: 18931.121 Å / C: 2675.2961 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Drosophila flam-del-412-St2;iso-1 ovary

EntireName: Drosophila flam-del-412-St2;iso-1 ovary
Components
  • Tissue: Drosophila flam-del-412-St2;iso-1 ovary

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Supramolecule #1: Drosophila flam-del-412-St2;iso-1 ovary

SupramoleculeName: Drosophila flam-del-412-St2;iso-1 ovary / type: tissue / ID: 1 / Parent: 0
Source (natural)Organism: Drosophila melanogaster (fruit fly) / Organ: Ovary

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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

BufferpH: 7
StainingType: POSITIVE / Material: Uranyl Acetate, Osmium Tetroxide
Details: 1% osmium tetroxide, 0.2% uranyl acetate (UA from Merck, Germany; OsO4 from EMS, USA).
Sugar embeddingMaterial: Epoxy resin / Details: Epoxy resin (Agar 100 from Agar Scientific, UK)
GridModel: Homemade / Material: COPPER / Mesh: 100 / Support film - Material: FORMVAR / Support film - topology: CONTINUOUS
VitrificationCryogen name: NITROGEN
High pressure freezingInstrument: OTHER
Details: HPF Compact 01 Engineering Office M. Wohlwend GmbH, Switzerland. The value given for _em_high_pressure_freezing.instrument is Wohlwend HPF Compact 01. This is not in a list of allowed values ...Details: HPF Compact 01 Engineering Office M. Wohlwend GmbH, Switzerland. The value given for _em_high_pressure_freezing.instrument is Wohlwend HPF Compact 01. This is not in a list of allowed values {'LEICA EM PACT2', 'EMS-002 RAPID IMMERSION FREEZER', 'OTHER', 'BAL-TEC HPM 010', 'LEICA EM PACT', 'LEICA EM HPM100'} so OTHER is written into the XML file.
Cryo protectantBSA
SectioningUltramicrotomy - Instrument: Leica UCT / Ultramicrotomy - Temperature: 293 K / Ultramicrotomy - Final thickness: 250
Ultramicrotomy - Details: Epoxy resin (Agar 100 from Agar Scientific, UK)
Fiducial markerManufacturer: Aurion / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TECNAI 20
DetailsC2 aperture diameter is 200 um
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 150.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 0.3 µm / Nominal defocus min: 0.15 µm / Nominal magnification: 19000
Sample stageSpecimen holder model: OTHER

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.9.3) / Number images used: 230
CTF correctionType: NONE

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