+Open data
-Basic information
Entry | Database: PDB / ID: 6taq | ||||||||||||
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Title | Structure of the dArc2 capsid | ||||||||||||
Components | Activity-regulated cytoskeleton associated protein 2 | ||||||||||||
Keywords | VIRUS LIKE PARTICLE / dArc / Gag / Virus / VLP | ||||||||||||
Function / homology | Ty3 transposon capsid-like protein / Ty3 transposon capsid-like protein / virus-like capsid / extracellular vesicle / structural molecule activity / RNA binding / identical protein binding / membrane / Activity-regulated cytoskeleton associated protein 2 Function and homology information | ||||||||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
Authors | Erlendsson, S. / Morado, D.R. / Shepherd, J.D. / Briggs, J.A.G. | ||||||||||||
Funding support | Denmark, United States, United Kingdom, 3items
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Citation | Journal: Nat Neurosci / Year: 2020 Title: Structures of virus-like capsids formed by the Drosophila neuronal Arc proteins. Authors: Simon Erlendsson / Dustin R Morado / Harrison B Cullen / Cedric Feschotte / Jason D Shepherd / John A G Briggs / Abstract: Arc, a neuronal gene that is critical for synaptic plasticity, originated through the domestication of retrotransposon Gag genes and mediates intercellular messenger RNA transfer. We report high- ...Arc, a neuronal gene that is critical for synaptic plasticity, originated through the domestication of retrotransposon Gag genes and mediates intercellular messenger RNA transfer. We report high-resolution structures of retrovirus-like capsids formed by Drosophila dArc1 and dArc2 that have surface spikes and putative internal RNA-binding domains. These data demonstrate that virus-like capsid-forming properties of Arc are evolutionarily conserved and provide a structural basis for understanding their function in intercellular communication. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6taq.cif.gz | 128.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6taq.ent.gz | 102.2 KB | Display | PDB format |
PDBx/mmJSON format | 6taq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6taq_validation.pdf.gz | 915.9 KB | Display | wwPDB validaton report |
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Full document | 6taq_full_validation.pdf.gz | 925.6 KB | Display | |
Data in XML | 6taq_validation.xml.gz | 27.3 KB | Display | |
Data in CIF | 6taq_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ta/6taq ftp://data.pdbj.org/pub/pdb/validation_reports/ta/6taq | HTTPS FTP |
-Related structure data
Related structure data | 10424MC 6tapC 6tarC 6tasC 6tatC 6tauC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 22656.734 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Arc2, CG13941 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7JV70 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: dArc2 Capsids / Type: CELL / Entity ID: all / Source: NATURAL | |||||||||||||||||||||||||
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21(DE3) / Plasmid: pGEX 4T1 | |||||||||||||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: dArc2 capsids are prepared from purified protein. | |||||||||||||||||||||||||
Specimen support | Details: 25 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Homemade | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 35 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Width: 4096 / Height: 4096 / Movie frames/image: 75 / Used frames/image: 1-75 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3573 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1779 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6GSE Accession code: 6GSE / Source name: PDB / Type: experimental model |