6YTU

Atomic-resolution structure of the coiled-coil dimerisation domain of human Arc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.124 
  • R-Value Work: 0.103 
  • R-Value Observed: 0.104 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Arc self-association and formation of virus-like capsids are mediated by an N-terminal helical coil motif.

Eriksen, M.S.Nikolaienko, O.Hallin, E.I.Grodem, S.Bustad, H.J.Flydal, M.I.Merski, I.Hosokawa, T.Lascu, D.Akerkar, S.Cuellar, J.Chambers, J.J.O'Connell, R.Muruganandam, G.Loris, R.Touma, C.Kanhema, T.Hayashi, Y.Stratton, M.M.Valpuesta, J.M.Kursula, P.Martinez, A.Bramham, C.R.

(2021) FEBS J 288: 2930-2955

  • DOI: https://doi.org/10.1111/febs.15618
  • Primary Citation of Related Structures:  
    6YTU

  • PubMed Abstract: 

    Activity-regulated cytoskeleton-associated protein (Arc) is a protein interaction hub with diverse roles in intracellular neuronal signaling, and important functions in neuronal synaptic plasticity, memory, and postnatal cortical development. Arc has homology to retroviral Gag protein and is capable of self-assembly into virus-like capsids implicated in the intercellular transfer of RNA. However, the molecular basis of Arc self-association and capsid formation is largely unknown. Here, we identified a 28-amino-acid stretch in the mammalian Arc N-terminal (NT) domain that is necessary and sufficient for self-association. Within this region, we identified a 7-residue oligomerization motif, critical for the formation of virus-like capsids. Purified wild-type Arc formed capsids as shown by transmission and cryo-electron microscopy, whereas mutant Arc with disruption of the oligomerization motif formed homogenous dimers. An atomic-resolution crystal structure of the oligomerization region peptide demonstrated an antiparallel coiled-coil interface, strongly supporting NT-NT domain interactions in Arc oligomerization. The NT coil-coil interaction was also validated in live neurons using fluorescence lifetime FRET imaging, and mutation of the oligomerization motif disrupted Arc-facilitated endocytosis. Furthermore, using single-molecule photobleaching, we show that Arc mRNA greatly enhances higher-order oligomerization in a manner dependent on the oligomerization motif. In conclusion, a helical coil in the Arc NT domain supports self-association above the dimer stage, mRNA-induced oligomerization, and formation of virus-like capsids. DATABASE: The coordinates and structure factors for crystallographic analysis of the oligomerization region were deposited at the Protein Data Bank with the entry code 6YTU.


  • Organizational Affiliation

    Department of Biomedicine, University of Bergen, Norway.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Activity-regulated cytoskeleton-associated protein
A, B
35Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for Q7LC44 (Homo sapiens)
Explore Q7LC44 
Go to UniProtKB:  Q7LC44
PHAROS:  Q7LC44
GTEx:  ENSG00000198576 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7LC44
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.124 
  • R-Value Work: 0.103 
  • R-Value Observed: 0.104 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 26.844α = 90
b = 42.556β = 90
c = 67.35γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Norwegian Research CouncilNorway--

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2021-05-12
    Changes: Database references