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- EMDB-19644: Tomographic reconstruction of the follicle cell nuclear periphery... -

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Basic information

Entry
Database: EMDB / ID: EMD-19644
TitleTomographic reconstruction of the follicle cell nuclear periphery from high pressure frozen, freeze substituted and resin embedded D. melanogaster egg chamber
Map data
Sample
  • Tissue: D. melanogaster egg chamber from tj>Sec31::RFP flies
KeywordsTomography / Drosophila / melanogaster / follicle cell / nuclear periphery / nucleus / freeze-substitution / VIRUS LIKE PARTICLE
Biological speciesDrosophila melanogaster (fruit fly)
Methodelectron tomography / cryo EM / negative staining
AuthorsKlumpe S / Hampoelz B / Ronchi P / Beck M / Plitzko J
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Cell / Year: 2025
Title: In-cell structure and snapshots of copia retrotransposons in intact tissue by cryo-ET.
Authors: Sven Klumpe / Kirsten A Senti / Florian Beck / Jenny Sachweh / Bernhard Hampoelz / Paolo Ronchi / Viola Oorschot / Marlene Brandstetter / Assa Yeroslaviz / John A G Briggs / Julius Brennecke ...Authors: Sven Klumpe / Kirsten A Senti / Florian Beck / Jenny Sachweh / Bernhard Hampoelz / Paolo Ronchi / Viola Oorschot / Marlene Brandstetter / Assa Yeroslaviz / John A G Briggs / Julius Brennecke / Martin Beck / Jürgen M Plitzko /
Abstract: Long terminal repeat (LTR) retrotransposons belong to the transposable elements (TEs), autonomously replicating genetic elements that integrate into the host's genome. Among animals, Drosophila ...Long terminal repeat (LTR) retrotransposons belong to the transposable elements (TEs), autonomously replicating genetic elements that integrate into the host's genome. Among animals, Drosophila melanogaster serves as an important model organism for TE research and contains several LTR retrotransposons, including the Ty1-copia family, which is evolutionarily related to retroviruses and forms virus-like particles (VLPs). In this study, we use cryo-focused ion beam (FIB) milling and lift-out approaches to visualize copia VLPs in ovarian cells and intact egg chambers, resolving the in situ copia capsid structure to 7.7 Å resolution by cryoelectron tomography (cryo-ET). Although cytoplasmic copia VLPs vary in size, nuclear VLPs are homogeneous and form densely packed clusters, supporting a model in which nuclear import acts as a size selector. Analyzing flies deficient in the TE-suppressing PIWI-interacting RNA (piRNA) pathway, we observe copia's translocation into the nucleus during spermatogenesis. Our findings provide insights into the replication cycle and cellular structural biology of an active LTR retrotransposon.
History
DepositionFeb 16, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19644.png

Downloads & links

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Map

FileDownload / File: emd_19644.map.gz / Format: CCP4 / Size: 1.5 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
12.2 Å/pix.
x 186 pix.
= 2269.2 Å		12.2 Å/pix.
x 2048 pix.
= 24985.6 Å		12.2 Å/pix.
x 2048 pix.
= 24985.6 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: 12.2 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-2291.0 - 2595.0
Average (Standard dev.)418.322749999999985 (±385.552829999999972)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-87
Dimensions20482048186
Spacing20482048186
CellA: 24985.6 Å / B: 24985.6 Å / C: 2269.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : D. melanogaster egg chamber from tj>Sec31::RFP flies

EntireName: D. melanogaster egg chamber from tj>Sec31::RFP flies
Components
  • Tissue: D. melanogaster egg chamber from tj>Sec31::RFP flies

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Supramolecule #1: D. melanogaster egg chamber from tj>Sec31::RFP flies

SupramoleculeName: D. melanogaster egg chamber from tj>Sec31::RFP flies / type: tissue / ID: 1 / Parent: 0
Details: Females from F1 scored against CyO from following genotypes: traffic jam-GAL4/CyO;; and w* P{UAS-Sec31.RFP}13.5; snaSco/CyO, P{ftz-lacB}E3 (Bloomington #86533);
Source (natural)Organism: Drosophila melanogaster (fruit fly) / Organ: Egg chamber / Tissue: Follicle cell epithelium

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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: 7.4
StainingType: NEGATIVE / Material: Uranyl Acetate
Sugar embeddingMaterial: Lowicryl HM20
VitrificationCryogen name: NITROGEN
DetailsDissected egg chambers
High pressure freezingInstrument: OTHER
Details: The value given for _em_high_pressure_freezing.instrument is HPM 010. This is not in a list of allowed values {'EMS-002 RAPID IMMERSION FREEZER', 'BAL-TEC HPM 010', 'OTHER', 'LEICA EM ...Details: The value given for _em_high_pressure_freezing.instrument is HPM 010. This is not in a list of allowed values {'EMS-002 RAPID IMMERSION FREEZER', 'BAL-TEC HPM 010', 'OTHER', 'LEICA EM HPM100', 'LEICA EM PACT2', 'LEICA EM PACT'} so OTHER is written into the XML file.
Cryo protectant20% Ficoll 70 kDa
SectioningUltramicrotomy - Instrument: Leica EM UC7 / Ultramicrotomy - Temperature: 293 K / Ultramicrotomy - Final thickness: 300

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: OTHER / Average electron dose: 10.0 e/Å2 / Details: Gatan OneView
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 121

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