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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10424 | ||||||||||||
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Title | Structure of the dArc2 capsid | ||||||||||||
![]() | dArc2 capsid | ||||||||||||
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![]() | dArc / Gag / Virus / VLP / VIRUS LIKE PARTICLE | ||||||||||||
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![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
![]() | Erlendsson S / Morado DR | ||||||||||||
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 | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 396.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.6 KB 16.6 KB | Display Display | ![]() |
Images | ![]() | 159.6 KB | ||
Filedesc metadata | ![]() | 6 KB | ||
Others | ![]() | 408.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6taqMC ![]() 6tapC ![]() 6tarC ![]() 6tasC ![]() 6tatC ![]() 6tauC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | dArc2 capsid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.388 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: dArc2 capsid unsharpened
File | emd_10424_additional.map | ||||||||||||
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Annotation | dArc2 capsid unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : dArc2 Capsids
Entire | Name: dArc2 Capsids |
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Components |
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-Supramolecule #1: dArc2 Capsids
Supramolecule | Name: dArc2 Capsids / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Activity-regulated cytoskeleton associated protein 2
Macromolecule | Name: Activity-regulated cytoskeleton associated protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 22.656734 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MTQMSDEQFR IFIETIKSLG PIKEEPPSKG SFSNCTVRFS GQRDHDAVDE FINAVETYKE VEGISDKDAL KGLPLLFKSI AVVWWKGVR RDAKTWSDAL QLLRDHFSPT KPSYQIYMEI FETKQSYDEV IDSFICKQRA LLAKLPEGRH DEETELDFIY G LMQPKYRE ...String: MTQMSDEQFR IFIETIKSLG PIKEEPPSKG SFSNCTVRFS GQRDHDAVDE FINAVETYKE VEGISDKDAL KGLPLLFKSI AVVWWKGVR RDAKTWSDAL QLLRDHFSPT KPSYQIYMEI FETKQSYDEV IDSFICKQRA LLAKLPEGRH DEETELDFIY G LMQPKYRE SIPRHEVKTF RELLDRGRTV ERTRH UniProtKB: Activity-regulated cytoskeleton associated protein 2 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.1 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Homemade / Material: COPPER / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: LACEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa / Details: 25 mA | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | dArc2 capsids are prepared from purified protein. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-75 / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |