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- EMDB-43584: Structure of the Drosophila retrotransposon Copia capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-43584
TitleStructure of the Drosophila retrotransposon Copia capsid
Map data
Sample
  • Complex: Copia Gag Capsid
    • Protein or peptide: Copia VLP protein
KeywordsDrosophila retrotransposon Copia / virus like particle / Gag protein
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 (fruit flies)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.17 Å
AuthorsLiu Y / Kelch BA
Funding support United States, 1 items
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
DepositionFeb 1, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43584.png

Downloads & links

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Map

FileDownload / File: emd_43584.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 560 pix.
= 751.68 Å		1.34 Å/pix.
x 560 pix.
= 751.68 Å		1.34 Å/pix.
x 560 pix.
= 751.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34229 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.177
Minimum - Maximum-0.19071564 - 0.579817
Average (Standard dev.)0.0021366922 (±0.044407904)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 751.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_43584_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43584_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Copia Gag Capsid

EntireName: Copia Gag Capsid
Components
  • Complex: Copia Gag Capsid
    • Protein or peptide: Copia VLP protein

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Supramolecule #1: Copia Gag Capsid

SupramoleculeName: Copia Gag Capsid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila (fruit flies)
Molecular weightTheoretical: 190 KDa

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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 (fruit flies)
Molecular weightTheoretical: 31.14899 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDKAKRNIKP FDGEKYAIWK FRIRALLAEQ DVLKVVDGLM PNEVDDSWKK AERCAKSTII EYLSDSFLNF ATSDITARQI LENLDAVYE RKSLASQLAL RKRLLSLKLS SEMSLLSHFH IFDELISELL AAGAKIEEMD KISHLLITLP SCYDGIITAI E TLSEENLT ...String:
MDKAKRNIKP FDGEKYAIWK FRIRALLAEQ DVLKVVDGLM PNEVDDSWKK AERCAKSTII EYLSDSFLNF ATSDITARQI LENLDAVYE RKSLASQLAL RKRLLSLKLS SEMSLLSHFH IFDELISELL AAGAKIEEMD KISHLLITLP SCYDGIITAI E TLSEENLT LAFVKNRLLD QEIKIKNDHN DTSKKVMNAI VHNNNNTYKN NLFKNRVTKP KKIFKGNSKY KVKCHHCGRE GH IKKDCFH YKRILNNKNK ENEKQVQTAT SHG

UniProtKB: Copia protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.8 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
25.0 mMHEPESHEPES
150.0 mMNaClsodium chloride
0.1 mMZnCl2zinc chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 35 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.98 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 45000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: Alphafold
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 5923
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: cryoSPARC

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8vwg:
Structure of the Drosophila retrotransposon Copia capsid

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