8S41 | pdb_00008s41

The structure of the copia retrotransposon icosahedral capsid (T=9)

• PDB DOI: https://doi.org/10.2210/pdb8S41/pdb
• EM Map EMD-19708: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2024-02-20 Released: 2025-03-05 
• Deposition Author(s): Klumpe, S., Beck, F., Briggs, J.A.G., Beck, M., Plitzko, J.M.
• Funding Organization(s): Max Planck Society

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 7.70 Å
• Aggregation State: CELL 
• Reconstruction Method: SUBTOMOGRAM AVERAGING 

Literature

In-cell structure and snapshots of copia retrotransposons in intact tissue by cryo-ET.

Klumpe, S., Senti, K.A., Beck, F., Sachweh, J., Hampoelz, B., Ronchi, P., Oorschot, V., Brandstetter, M., Yeroslaviz, A., Briggs, J.A.G., Brennecke, J., Beck, M., Plitzko, J.M.

(2025) Cell 188: 2094

• PubMed: 40049165 
• DOI: https://doi.org/10.1016/j.cell.2025.02.003
• Primary Citation of Related Structures:  
  8S41


• PubMed 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 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.

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Organizational Affiliation: 
• Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany. Electronic address: [e-mail].
Institute of Molecular Biotechnology Austria (IMBA), Vienna, Austria.
Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany.
Department Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany.
EMBL EM Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
Electron Microscopy Facility, Vienna BioCenter Core Facilities, Vienna, Austria.
Computational Systems Biochemistry, Bioinformatics Core Facility, Max Planck Institute of Biochemistry, Martinsried, Germany.
Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany.
Institute of Molecular Biotechnology Austria (IMBA), Vienna, Austria. Electronic address: [e-mail].
Department Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany; Institute of Biochemistry, Goethe University Frankfurt, Frankfurt, Germany. Electronic address: [e-mail].
Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 540-mer - A540 

Biological assembly 1 assigned by authors and generated by UCSF CHIMERA 1.14_b42094. (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 192.61 kDa 
• Atom Count: 13,509 
• Modeled Residue Count: 1,683 
• Deposited Residue Count: 1,683 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copia VLP protein	A, B [auth F], C [auth G], D [auth L], E [auth Q], F [auth V], G [auth X], H [auth a], I [auth d]	187	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for P04146 (Drosophila melanogaster) Explore P04146  Go to UniProtKB:  P04146

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 7.70 Å
• Aggregation State: CELL 
• Reconstruction Method: SUBTOMOGRAM AVERAGING 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX	1.20.1-4487

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-05 
Deposition Author(s): Klumpe, S., Beck, F., Briggs, J.A.G., Beck, M., Plitzko, J.M.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History  

• Version 1.0: 2025-03-05
  Type: Initial release
  
• Version 1.1: 2025-03-19
  Changes: Data collection, Database references
• Version 1.2: 2025-04-30
  Changes: Data collection, Database references