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- PDB-8vw3: Structure of the non-symmetric capsomer of the Drosophila retrotr... -

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Basic information

Entry
Database: PDB / ID: 8vw3
TitleStructure of the non-symmetric capsomer of the Drosophila retrotransposon Copia capsid
ComponentsCopia VLP protein
KeywordsVIRUS LIKE PARTICLE / Drosophila retrotransposon Copia / Gag protein
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 (fruit flies)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsLiu, Y. / Kelch, B.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: PLoS Biol / Year: 2025
Title: Capsid transfer of the retrotransposon Copia controls structural synaptic plasticity in Drosophila.
Authors: P Githure M'Angale / Adrienne Lemieux / Yumeng Liu / Shuhao Wang / Max Zinter / Gimena Alegre / Alfred Simkin / Vivian Budnik / Brian A Kelch / Travis Thomson /
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 ...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.
History
DepositionJan 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Copia VLP protein
B: Copia VLP protein
C: Copia VLP protein
D: Copia VLP protein
E: Copia VLP protein
F: Copia VLP protein


Theoretical massNumber of molelcules
Total (without water)186,8946
Polymers186,8946
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Copia VLP protein


Mass: 31148.990 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila (fruit flies) / Gene: GIP, COPIA / Production host: Escherichia coli (E. coli) / References: UniProt: P04146
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Copia Gag capsid non-symmetric capsomer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.13 MDa / Experimental value: NO
Source (natural)Organism: Drosophila (fruit flies)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESHEPES1
2150 mMsodium chlorideNaCl1
30.1 mMzinc chlorideZnCl21
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283.15 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 X / Nominal defocus max: 2900 nm / Nominal defocus min: 300 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 39.98 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
7Cootmodel fitting
9PHENIXmodel refinement
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 355380 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028982
ELECTRON MICROSCOPYf_angle_d0.36712096
ELECTRON MICROSCOPYf_dihedral_angle_d2.9581176
ELECTRON MICROSCOPYf_chiral_restr0.0341428
ELECTRON MICROSCOPYf_plane_restr0.0021512

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