+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10426 | ||||||||||||
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Title | Structure of the two-fold capsomer of the dArc1 capsid | ||||||||||||
Map data | dArc1 two-fold capsomer | ||||||||||||
Sample |
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Function / homology | Function and homology information postsynapse of neuromuscular junction / muscle system process / behavioral response to starvation / vesicle-mediated intercellular transport / regulation of neuronal synaptic plasticity / mRNA transport / sarcomere / extracellular vesicle / mRNA binding / synapse ...postsynapse of neuromuscular junction / muscle system process / behavioral response to starvation / vesicle-mediated intercellular transport / regulation of neuronal synaptic plasticity / mRNA transport / sarcomere / extracellular vesicle / mRNA binding / synapse / membrane / identical protein binding Similarity search - Function | ||||||||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.75 Å | ||||||||||||
Authors | Erlendsson S / Morado DR / Shepherd JD / Briggs JAG | ||||||||||||
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_10426.map.gz | 8.8 MB | EMDB map data format | |
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Header (meta data) | emd-10426-v30.xml emd-10426.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
Images | emd_10426.png | 72.6 KB | ||
Others | emd_10426_additional.map.gz | 9.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10426 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10426 | HTTPS FTP |
-Related structure data
Related structure data | 6tasMC 6tapC 6taqC 6tarC 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_10426.map.gz / Format: CCP4 / Size: 12.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | dArc1 two-fold capsomer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 two-fold capsomer unsharpened
File | emd_10426_additional.map | ||||||||||||
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Annotation | dArc1 two-fold capsomer 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 Details: The two-fold dArc1 capsomer map is generated by symmetry expansion, sub-boxing and local refinement. |
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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: 8 / 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 |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 2 / 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 - 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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 2266380 Details: From 37773 initial dArc1 icosahedral capsids, we performed symmetry expansion as implemented in RELION, to calculate the positions and orientations for each of the 2,266,380 asymmetric units ...Details: From 37773 initial dArc1 icosahedral capsids, we performed symmetry expansion as implemented in RELION, to calculate the positions and orientations for each of the 2,266,380 asymmetric units for dArc1, centered at the two-fold hexametric capsomeres. We extracted individual capsomeres using a box size of 148 pixels. | ||||||
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CTF correction | Software:
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3) | ||||||
Final 3D classification | Number classes: 8 / Software - Name: RELION (ver. 3) / Details: See Materials & Methods | ||||||
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3) | ||||||
Final reconstruction | Number classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 1685349 |