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- EMDB-19647: Tomographic reconstruction of nuclear copia VLP clusters in D. me... -

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Basic information

Entry
Database: EMDB / ID: EMD-19647
TitleTomographic reconstruction of nuclear copia VLP clusters in D. melanogaster ovarian somatic cells
Map dataTomographic reconstruction of nuclear copia VLP clusters
Sample
  • Complex: Copia retrotransposon capsid
KeywordsTomography / Drosophila / melanogaster / follicle cell / ovarian soma / copia / Ty1 / retrotransposon / LTR / VIRUS LIKE PARTICLE
Biological speciesDrosophila melanogaster (fruit fly)
Methodelectron tomography / cryo EM
AuthorsKlumpe S / Beck F / Briggs JAG / Beck M / Plitzko JM
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_19647.png

Downloads & links

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Map

FileDownload / File: emd_19647.map.gz / Format: CCP4 / Size: 2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomographic reconstruction of nuclear copia VLP clusters
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
11.84 Å/pix.
x 512 pix.
= 6062.08 Å		11.84 Å/pix.
x 1024 pix.
= 12124.16 Å		11.84 Å/pix.
x 1024 pix.
= 12124.16 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: 11.84 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-3205.727300000000014 - 2078.344200000000001
Average (Standard dev.)-0.2000174 (±234.679059999999993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions10241024512
Spacing10241024512
CellA: 12124.16 Å / B: 12124.16 Å / C: 6062.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Copia retrotransposon capsid

EntireName: Copia retrotransposon capsid
Components
  • Complex: Copia retrotransposon capsid

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Supramolecule #1: Copia retrotransposon capsid

SupramoleculeName: Copia retrotransposon capsid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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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
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.1 / Focused ion beam - Duration: 100 / Focused ion beam - Temperature: 93 K / Focused ion beam - Initial thickness: 5000 / Focused ion beam - Final thickness: 150
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is FEI Aquilos 1. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 4.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 30

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