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- EMDB-10424: Structure of the dArc2 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-10424
TitleStructure of the dArc2 capsid
Map datadArc2 capsid
Sample
  • Cell: dArc2 Capsids
    • Protein or peptide: Activity-regulated cytoskeleton associated protein 2
KeywordsdArc / Gag / Virus / VLP / VIRUS LIKE PARTICLE
Function / homologyTy3 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 speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsErlendsson S / Morado DR
Funding support Denmark, United States, United Kingdom, 3 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17OC0030788 Denmark
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01-MH112766 United States
Medical Research Council (United Kingdom)MC_UP_1201/16 United Kingdom
CitationJournal: 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
DepositionOct 30, 2019-
Header (metadata) releaseJan 1, 2020-
Map releaseJan 1, 2020-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6taq
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6taq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10424.png

Downloads & links

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Map

FileDownload / File: emd_10424.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdArc2 capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 512 pix.
= 710.656 Å		1.39 Å/pix.
x 512 pix.
= 710.656 Å		1.39 Å/pix.
x 512 pix.
= 710.656 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.388 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.0022013749 - 0.18697459
Average (Standard dev.)0.00034479875 (±0.0050533605)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 710.656 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3881.3881.388
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z710.656710.656710.656
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0020.1870.000

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Supplemental data

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Additional map: dArc2 capsid unsharpened

Fileemd_10424_additional.map
AnnotationdArc2 capsid unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : dArc2 Capsids

EntireName: dArc2 Capsids
Components
  • Cell: dArc2 Capsids
    • Protein or peptide: Activity-regulated cytoskeleton associated protein 2

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Supramolecule #1: dArc2 Capsids

SupramoleculeName: dArc2 Capsids / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Activity-regulated cytoskeleton associated protein 2

MacromoleculeName: Activity-regulated cytoskeleton associated protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 22.656734 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
50.0 mMC4H11NO3Tris
1.0 mMC4H10O2S2DTT
50.0 uMZnCl2zinc cloride
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV
DetailsdArc2 capsids are prepared from purified protein.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3573
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 1779
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final 3D classificationDetails: See Materials & Methods

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Atomic model buiding 1

Initial modelPDB ID:

6gse


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6taq:
Structure of the dArc2 capsid

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