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- PDB-6tar: Structure of the five-fold capsomer of the dArc1 capsid -

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Basic information

Entry
Database: PDB / ID: 6tar
TitleStructure of the five-fold capsomer of the dArc1 capsid
ComponentsActivity-regulated cytoskeleton associated protein 1
KeywordsVIRUS LIKE PARTICLE / dArc / Gag / Virus / VLP
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsErlendsson, S. / Morado, D.R. / Shepherd, J.D. / Briggs, J.A.G.
Funding support Denmark, United States, United Kingdom, 3items
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, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Jul 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Assembly

Deposited unit
A: Activity-regulated cytoskeleton associated protein 1
B: Activity-regulated cytoskeleton associated protein 1
C: Activity-regulated cytoskeleton associated protein 1
D: Activity-regulated cytoskeleton associated protein 1
E: Activity-regulated cytoskeleton associated protein 1


Theoretical massNumber of molelcules
Total (without water)144,6065
Polymers144,6065
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area9260 Å2
ΔGint-19 kcal/mol
Surface area50060 Å2
MethodPISA

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Components

#1: Protein
Activity-regulated cytoskeleton associated protein 1 / dArc1


Mass: 28921.201 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Arc1, CG12505 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7K1U0

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: dArc1 capsids / Type: CELL
Details: The five-fold dArc1 capsomer map is generated by symmetry expansion, sub-boxing and local refinement.
Entity ID: all / Source: NATURAL
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3) / Plasmid: pGEX 4T1
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
250 mMTrisC4H11NO31
31 mMDTTC4H10O2S21
450 uMzinc clorideZnCl21
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: dArc1 capsids
Specimen supportDetails: 25 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Homemade
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 35 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 75 / Used frames/image: 1-75

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Processing

EM software
IDNameVersionCategoryDetails
1RELION3particle selection
2SerialEM3.6image acquisition
3DigitalMicrographimage acquisition
5RELION3CTF correction
6CTFFIND4CTF correctionDefoci Estimation
9PHENIX1.16model fitting
10Coot0.8.9.1model fitting
11UCSF Chimera1.13.1model fitting
13PHENIX1.16model refinement
14RELION3initial Euler assignment
15RELION3final Euler assignment
17RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 453276
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 five-fold capsomeres. We extracted individual capsomeres using a box size of 148 pixels. For the five-fold capsomeres we removed the redundant five-fold symmetrized capsomeres leaving 453,276 particles.
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 453276 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingPDB-ID: 6GSE

6gse


Accession code: 6GSE / Source name: PDB / Type: experimental model

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