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- EMDB-19708: The structure of the copia retrotransposon icosahedral capsid (T=9) -

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Basic information

Entry
Database: EMDB / ID: EMD-19708
TitleThe structure of the copia retrotransposon icosahedral capsid (T=9)
Map dataMain postprocessed map
Sample
  • Complex: Copia retrotransposon capsid
    • Protein or peptide: Copia VLP protein
KeywordsTomography / Drosophila / melanogaster / follicle cell / copia / Ty1 / retrotransposon / LTR / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


DNA polymerase complex / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA biosynthetic process / DNA integration / aspartic-type endopeptidase activity / nucleic acid binding / proteolysis / zinc ion binding / ATP binding
Similarity search - Function
GAG-pre-integrase domain / : / GAG-pre-integrase domain / gag-polypeptide of LTR copia-type / Pol polyprotein, beta-barrel domain / : / Reverse transcriptase, RNA-dependent DNA polymerase / Reverse transcriptase (RNA-dependent DNA polymerase) / Integrase core domain / Integrase, catalytic core ...GAG-pre-integrase domain / : / GAG-pre-integrase domain / gag-polypeptide of LTR copia-type / Pol polyprotein, beta-barrel domain / : / Reverse transcriptase, RNA-dependent DNA polymerase / Reverse transcriptase (RNA-dependent DNA polymerase) / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
Methodsubtomogram averaging / cryo EM / Resolution: 7.7 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 20, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19708.png

Downloads & links

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Map

FileDownload / File: emd_19708.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain postprocessed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.54 Å/pix.
x 256 pix.
= 650.24 Å		2.54 Å/pix.
x 256 pix.
= 650.24 Å		2.54 Å/pix.
x 256 pix.
= 650.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.54 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-0.673441 - 2.2258365
Average (Standard dev.)0.068148896 (±0.26953828)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 650.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19708_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Additional map: Postprocessed masked map

Fileemd_19708_additional_1.map
AnnotationPostprocessed masked map
Projections & Slices
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Histogram

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Half map: Half map 1

Fileemd_19708_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_19708_half_map_2.map
AnnotationHalf map 2
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Sample components

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Entire : Copia retrotransposon capsid

EntireName: Copia retrotransposon capsid
Components
  • Complex: Copia retrotransposon capsid
    • Protein or peptide: Copia VLP protein

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Supramolecule #1: Copia retrotransposon capsid

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

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Macromolecule #1: Copia VLP protein

MacromoleculeName: Copia VLP protein / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 21.400764 KDa
SequenceString:
MDKAKRNIKP FDGEKYAIWK FRIRALLAEQ DVLKVVDGLM PNEVDDSWKK AERCAKSTII EYLSDSFLNF ATSDITARQI LENLDAVYE RKSLASQLAL RKRLLSLKLS SEMSLLSHFH IFDELISELL AAGAKIEEMD KISHLLITLP SCYDGIITAI E TLSEENLT LAFVKNRLLD QEIKIKNDH

UniProtKB: Copia protein

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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: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 735
ExtractionNumber tomograms: 3 / Number images used: 1780 / Software - Name: STOPGAP (ver. 0.7)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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