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- EMDB-19649: In situ copia VLP cluster subtomogram averaging, C1-C1 contact map -

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Basic information

Entry
Database: EMDB / ID: EMD-19649
TitleIn situ copia VLP cluster subtomogram averaging, C1-C1 contact map
Map dataPostprocessed map low-pass filtered to 35 A (FSC 0.5)
Sample
  • Complex: Copia retrotransposon capsid
KeywordsTomography / Drosophila / melanogaster / follicle cell / copia / Ty1 / retrotransposon / LTR / VIRUS LIKE PARTICLE
Biological speciesDrosophila melanogaster (fruit fly)
Methodsubtomogram averaging / cryo EM / Resolution: 35.0 Å
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_19649.png

Downloads & links

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Map

FileDownload / File: emd_19649.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map low-pass filtered to 35 A (FSC 0.5)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.24 Å/pix.
x 168 pix.
= 376.32 Å		2.24 Å/pix.
x 168 pix.
= 376.32 Å		2.24 Å/pix.
x 168 pix.
= 376.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.46146503 - 0.5167241
Average (Standard dev.)0.014152194 (±0.17356479)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 376.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1

Fileemd_19649_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_19649_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE

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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: 5.0 µm / Nominal defocus min: 3.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION / Number subtomograms used: 946
ExtractionNumber tomograms: 3 / Number images used: 946
Final 3D classificationNumber classes: 4
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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