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Open data
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Basic information
Entry | Database: PDB / ID: 6tat | ||||||||||||
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Title | Structure of the five-fold capsomer of the dArc2 capsid | ||||||||||||
![]() | Activity-regulated cytoskeleton associated protein 2 | ||||||||||||
![]() | 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 / membrane / identical protein binding / Activity-regulated cytoskeleton associated protein 2![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
![]() | Erlendsson, S. / Morado, D.R. / Shepherd, J.D. / Briggs, J.A.G. | ||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150.6 KB | Display | ![]() |
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PDB format | ![]() | 125.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 748.4 KB | Display | ![]() |
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Full document | ![]() | 752.8 KB | Display | |
Data in XML | ![]() | 27.4 KB | Display | |
Data in CIF | ![]() | 35.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 10427MC ![]() 6tapC ![]() 6taqC ![]() 6tarC ![]() 6tasC ![]() 6tauC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 22656.734 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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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 |
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Sample preparation
Component | Name: dArc2 Capsids / Type: CELL Details: The five-fold dArc2 capsomer map is generated by symmetry expansion, sub-boxing and local refinement. Entity ID: all / Source: NATURAL | |||||||||||||||||||||||||
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Source (natural) | Organism: ![]() ![]() | |||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | |||||||||||||||||||||||||
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 | |||||||||||||||||||||||||
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 |
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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: ![]() |
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 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 21348 Details: From 1779 initial dArc2 icosahedral capsids, we performed symmetry expansion as implemented in RELION, to calculate the positions and orientations for each of the 106,740 asymmetric units ...Details: From 1779 initial dArc2 icosahedral capsids, we performed symmetry expansion as implemented in RELION, to calculate the positions and orientations for each of the 106,740 asymmetric units for dArc2, centered at the five-fold capsomeres. We extracted individual capsomeres using a box size of 148 pixels. For the five-fold capsomeres we removed the redundant five-fold symmetrized capsomeres leaving 21,348 particles. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C5 (5 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21348 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6GSE |