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- EMDB-10426: Structure of the two-fold capsomer of the dArc1 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-10426
TitleStructure of the two-fold capsomer of the dArc1 capsid
Map datadArc1 two-fold capsomer
Sample
  • Cell: dArc1 capsids
    • Protein or peptide: Activity-regulated cytoskeleton associated protein 1
  • Ligand: ZINC ION
KeywordsdArc / 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
Activity-regulated cytoskeleton associated protein 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 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: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tas
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6tas
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10426.png

Downloads & links

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Map

FileDownload / File: emd_10426.map.gz / Format: CCP4 / Size: 12.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdArc1 two-fold capsomer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.21 Å/pix.
x 148 pix.
= 179.228 Å		1.21 Å/pix.
x 148 pix.
= 179.228 Å		1.21 Å/pix.
x 148 pix.
= 179.228 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.211 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.0065100417 - 0.38397154
Average (Standard dev.)0.001325837 (±0.012711946)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions148148148
Spacing148148148
CellA=B=C: 179.228 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2111.2111.211
M x/y/z148148148
origin x/y/z0.0000.0000.000
length x/y/z179.228179.228179.228
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS148148148
D min/max/mean-0.0070.3840.001

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Supplemental data

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Additional map: dArc1 two-fold capsomer unsharpened

Fileemd_10426_additional.map
AnnotationdArc1 two-fold capsomer 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 : dArc1 capsids

EntireName: dArc1 capsids
Components
  • Cell: dArc1 capsids
    • Protein or peptide: Activity-regulated cytoskeleton associated protein 1
  • Ligand: ZINC ION

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Supramolecule #1: dArc1 capsids

SupramoleculeName: 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.
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Activity-regulated cytoskeleton associated protein 1

MacromoleculeName: Activity-regulated cytoskeleton associated protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 28.921201 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration0.5 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
DetailsdArc1 capsids

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / 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: 4.0 µm / Nominal defocus min: 1.0 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: 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.
Startup modelType of model: NONE
Final reconstructionNumber 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
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final 3D classificationNumber classes: 8 / Software - Name: RELION (ver. 3) / Details: 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-6tas:
Structure of the two-fold capsomer of the dArc1 capsid

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