+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10423 | ||||||||||||
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Title | Structure of the dArc1 capsid | ||||||||||||
Map data | dArc1 Capsid | ||||||||||||
Sample |
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Keywords | dArc / Gag / Virus / VLP / VIRUS LIKE PARTICLE | ||||||||||||
Function / homology | Function and homology information postsynapse of neuromuscular junction / muscle system process / behavioral response to starvation / virus-like capsid / vesicle-mediated intercellular transport / regulation of neuronal synaptic plasticity / mRNA transport / sarcomere / extracellular vesicle / mRNA binding ...postsynapse of neuromuscular junction / muscle system process / behavioral response to starvation / virus-like capsid / vesicle-mediated intercellular transport / regulation of neuronal synaptic plasticity / mRNA transport / sarcomere / extracellular vesicle / mRNA binding / synapse / structural molecule activity / identical protein binding / membrane Similarity search - Function | ||||||||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
Authors | Erlendsson S / Morado DR | ||||||||||||
Funding support | Denmark, United States, United Kingdom, 3 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10423.map.gz | 340.1 MB | EMDB map data format | |
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Header (meta data) | emd-10423-v30.xml emd-10423.xml | 17 KB 17 KB | Display Display | EMDB header |
Images | emd_10423.png | 163.2 KB | ||
Filedesc metadata | emd-10423.cif.gz | 6.2 KB | ||
Others | emd_10423_additional.map.gz | 404.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10423 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10423 | HTTPS FTP |
-Validation report
Summary document | emd_10423_validation.pdf.gz | 552.2 KB | Display | EMDB validaton report |
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Full document | emd_10423_full_validation.pdf.gz | 551.7 KB | Display | |
Data in XML | emd_10423_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | emd_10423_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10423 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10423 | HTTPS FTP |
-Related structure data
Related structure data | 6tapMC 6taqC 6tarC 6tasC 6tatC 6tauC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10423.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | dArc1 Capsid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.211 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: dArc1 Capsid unsharpened
File | emd_10423_additional.map | ||||||||||||
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Annotation | dArc1 Capsid unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : dArc1 Capsids
Entire | Name: dArc1 Capsids |
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Components |
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-Supramolecule #1: dArc1 Capsids
Supramolecule | Name: dArc1 Capsids / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
-Macromolecule #1: Activity-regulated cytoskeleton associated protein 1
Macromolecule | Name: Activity-regulated cytoskeleton associated protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 28.921201 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MAQLTQMTNE QLRELIEAVR AAAVGAAGSA AAAGGADASR GKGNFSACTH SFGGTRDHDV VEEFIGNIET YKDVEGISDE NALKGISLL FYGMASTWWQ GVRKEATTWK EAIALIREHF SPTKPAYQIY MEFFQNKQDD HDPIDTFVIQ KRALLAQLPS G RHDEETEL ...String: MAQLTQMTNE QLRELIEAVR AAAVGAAGSA AAAGGADASR GKGNFSACTH SFGGTRDHDV VEEFIGNIET YKDVEGISDE NALKGISLL FYGMASTWWQ GVRKEATTWK EAIALIREHF SPTKPAYQIY MEFFQNKQDD HDPIDTFVIQ KRALLAQLPS G RHDEETEL DLLFGLLNIK YRKHISRHSV HTFKDLLEQG RIIEHNNQED EEQLATAKNT RGSKRTTRCT YCSFRGHTFD NC RKRQKDR QEEQHEE UniProtKB: Activity-regulated cytoskeleton associated protein 1 |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 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 | dArc1 capsids are prepared from purified protein. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / 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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 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 |