8VW3 | pdb_00008vw3

Structure of the non-symmetric capsomer of the Drosophila retrotransposon Copia capsid


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Capsid transfer of the retrotransposon Copia controls structural synaptic plasticity in Drosophila.

M'Angale, P.G.Lemieux, A.Liu, Y.Wang, S.Zinter, M.Alegre, G.Simkin, A.Budnik, V.Kelch, B.A.Thomson, T.

(2025) PLoS Biol 23: e3002983-e3002983

  • DOI: https://doi.org/10.1371/journal.pbio.3002983
  • Primary Citation of Related Structures:  
    8VVW, 8VVZ, 8VW3, 8VWG

  • PubMed Abstract: 

    Transposons are parasitic genome elements that can also serve as raw material for the evolution of new cellular functions. However, how retrotransposons are selected and domesticated by host organisms to modulate synaptic plasticity remains largely unknown. Here, we show that the Ty1 retrotransposon Copia forms virus-like capsids in vivo and transfers between cells. Copia is enriched at the Drosophila neuromuscular junction (NMJ) and transported across synapses, and disrupting its expression promotes both synapse development and structural synaptic plasticity. We show that proper synaptic plasticity is maintained in Drosophila by the balance of Copia and the Arc1 (activity-regulated cytoskeleton-associated protein) homolog. High-resolution cryogenic-electron microscopy imaging shows that the structure of the Copia capsid has a large capacity and pores like retroviruses but is distinct from domesticated capsids such as dArc1. Our results suggest a fully functional transposon mediates synaptic plasticity, possibly representing an early stage of domestication of a retrotransposon.


  • Organizational Affiliation

    Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Copia VLP protein
A, B, C, D, E
270DrosophilaMutation(s): 0 
Gene Names: GIPCOPIA
UniProt
Find proteins for P04146 (Drosophila melanogaster)
Explore P04146 
Go to UniProtKB:  P04146
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04146
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Data collection, Database references