6S7X

dARC1 capsid domain dimer, orthorhombic form at 1.7 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure ofDrosophila melanogasterARC1 reveals a repurposed molecule with characteristics of retroviral Gag.

Cottee, M.A.Letham, S.C.Young, G.R.Stoye, J.P.Taylor, I.A.

(2020) Sci Adv 6: eaay6354-eaay6354

  • DOI: https://doi.org/10.1126/sciadv.aay6354
  • Primary Citation of Related Structures:  
    6S7X, 6S7Y

  • PubMed Abstract: 

    The tetrapod neuronal protein ARC and its Drosophila melanogaster homolog, dARC1, have important but differing roles in neuronal development. Both are thought to originate through exaptation of ancient Ty3/Gypsy retrotransposon Gag, with their novel function relying on an original capacity for self-assembly and encapsidation of nucleic acids. Here, we present the crystal structure of dARC1 CA and examine the relationship between dARC1, mammalian ARC, and the CA protein of circulating retroviruses. We show that while the overall architecture is highly related to that of orthoretroviral and spumaretroviral CA, there are substantial deviations in both amino- and carboxyl-terminal domains, potentially affecting recruitment of partner proteins and particle assembly. The degree of sequence and structural divergence suggests that Ty3/Gypsy Gag has been exapted on two separate occasions and that, although mammalian ARC and dARC1 share functional similarity, the structures have undergone different adaptations after appropriation into the tetrapod and insect genomes.


  • Organizational Affiliation

    Macromolecular Structure Laboratory, The Francis Crick Institute, Midland Road, London NW1 1AT, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Activity-regulated cytoskeleton associated protein 1
A, B
170Drosophila melanogasterMutation(s): 0 
Gene Names: Arc1CG12505
UniProt
Find proteins for Q7K1U0 (Drosophila melanogaster)
Explore Q7K1U0 
Go to UniProtKB:  Q7K1U0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7K1U0
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.334α = 90
b = 70.386β = 90
c = 142.821γ = 90
Software Package:
Software NamePurpose
AutoPROCdata scaling
XDSdata reduction
XSCALEdata scaling
pointlessdata scaling
Aimlessdata scaling
TRUNCATEdata reduction
STARANISOdata scaling
AutoSolphasing
BUCCANEERmodel building
Cootmodel building
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomFC001162, FC001178
Medical Research Council (United Kingdom)United KingdomFC001162, FC001178
Wellcome TrustUnited KingdomFC001162, FC001178
Wellcome TrustUnited Kingdom108014/Z/15/Z
Wellcome TrustUnited Kingdom108012/Z/15/Z

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references