6TAP

Structure of the dArc1 capsid

• PDB DOI: https://doi.org/10.2210/pdb6TAP/pdb
• EM Map EMD-10423: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-10-30 Released: 2020-01-01 
• Deposition Author(s): Erlendsson, S., Morado, D.R., Shepherd, J.D., Briggs, J.A.G.
• Funding Organization(s): Novo Nordisk Foundation, National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI), Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structures of virus-like capsids formed by the Drosophila neuronal Arc proteins.

Erlendsson, S., Morado, D.R., Cullen, H.B., Feschotte, C., Shepherd, J.D., Briggs, J.A.G.

(2020) Nat Neurosci 23: 172-175

• PubMed: 31907439 
• DOI: https://doi.org/10.1038/s41593-019-0569-y
• Primary Citation of Related Structures:  
  6TAP, 6TAQ, 6TAR, 6TAS, 6TAT, 6TAU


• PubMed 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-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.

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Organizational Affiliation: 

Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 300-mer - A240B60 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 144.67 kDa 
• Atom Count: 5,619 
• Modelled Residue Count: 686 
• Deposited Residue Count: 1,270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Activity-regulated cytoskeleton associated protein 1	A, B, C, D, E	254	Drosophila melanogaster	Mutation(s): 0  Gene Names: Arc1, CG12505
UniProt
Find proteins for Q7K1U0 (Drosophila melanogaster) Explore Q7K1U0  Go to UniProtKB:  Q7K1U0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	F [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.16
MODEL REFINEMENT	REFMAC	5
RECONSTRUCTION	RELION	3

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-01 
Deposition Author(s): Erlendsson, S., Morado, D.R., Shepherd, J.D., Briggs, J.A.G.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF17OC0030788
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R01-MH112766
Medical Research Council (United Kingdom)	United Kingdom	MC_UP_1201/16

Revision History  

• Version 1.0: 2020-01-01
  Type: Initial release
  
• Version 1.1: 2020-01-15
  Changes: Database references
• Version 1.2: 2020-02-19
  Changes: Database references
• Version 1.3: 2022-03-30
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2024-07-10
  Changes: Data collection, Refinement description