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- PDB-8s41: The structure of the copia retrotransposon icosahedral capsid (T=9) -

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Basic information

Entry
Database: PDB / ID: 8s41
TitleThe structure of the copia retrotransposon icosahedral capsid (T=9)
ComponentsCopia VLP protein
KeywordsVIRUS LIKE PARTICLE / Tomography / Drosophila / melanogaster / follicle cell / copia / Ty1 / retrotransposon / LTR
Function / homology
Function and homology information


DNA polymerase complex / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA biosynthetic process / DNA integration / nucleic acid binding / aspartic-type endopeptidase activity / 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)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 7.7 Å
AuthorsKlumpe, S. / Beck, F. / Briggs, J.A.G. / Beck, M. / Plitzko, J.M.
Funding support Germany, 1items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.1Mar 19, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Copia VLP protein
F: Copia VLP protein
G: Copia VLP protein
L: Copia VLP protein
Q: Copia VLP protein
V: Copia VLP protein
X: Copia VLP protein
a: Copia VLP protein
d: Copia VLP protein


Theoretical massNumber of molelcules
Total (without water)192,6079
Polymers192,6079
Non-polymers00
Water00
1
A: Copia VLP protein
F: Copia VLP protein
G: Copia VLP protein
L: Copia VLP protein
Q: Copia VLP protein
V: Copia VLP protein
X: Copia VLP protein
a: Copia VLP protein
d: Copia VLP protein
x 60


Theoretical massNumber of molelcules
Total (without water)11,556,413540
Polymers11,556,413540
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
MethodUCSF CHIMERA

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Components

#1: Protein
Copia VLP protein


Mass: 21400.764 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P04146
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Copia retrotransposon capsid / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 3500 nm
Image recordingElectron dose: 3 e/Å2 / Avg electron dose per subtomogram: 120 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1STOPGAP0.7volume selection
2FEI tomographyimage acquisition
4WarpCTF correction
7ISOLDE1.5model fitting
10RELION3.1final Euler assignment
12RELION3.1classification
13RELION3D reconstruction
20PHENIX1.20.1-4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 735 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 3 / Num. of volumes extracted: 1780

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