4X3I

The crystal structure of Arc N-lobe complexed with CAMK2A fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of arc binding to synaptic proteins: implications for cognitive disease.

Zhang, W.Wu, J.Ward, M.D.Yang, S.Chuang, Y.A.Xiao, M.Li, R.Leahy, D.J.Worley, P.F.

(2015) Neuron 86: 490-500

  • DOI: https://doi.org/10.1016/j.neuron.2015.03.030
  • Primary Citation of Related Structures:  
    4X3H, 4X3I, 4X3X

  • PubMed Abstract: 

    Arc is a cellular immediate-early gene (IEG) that functions at excitatory synapses and is required for learning and memory. We report crystal structures of Arc subdomains that form a bi-lobar architecture remarkably similar to the capsid domain of human immunodeficiency virus (HIV) gag protein. Analysis indicates Arc originated from the Ty3/Gypsy retrotransposon family and was "domesticated" in higher vertebrates for synaptic functions. The Arc N-terminal lobe evolved a unique hydrophobic pocket that mediates intermolecular binding with synaptic proteins as resolved in complexes with TARPγ2 (Stargazin) and CaMKII peptides and is essential for Arc's synaptic function. A consensus sequence for Arc binding identifies several additional partners that include genes implicated in schizophrenia. Arc N-lobe binding is inhibited by small chemicals suggesting Arc's synaptic action may be druggable. These studies reveal the remarkable evolutionary origin of Arc and provide a structural basis for understanding Arc's contribution to neural plasticity and disease.


  • Organizational Affiliation

    Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Activity-regulated cytoskeleton-associated protein79Rattus norvegicusMutation(s): 0 
Gene Names: Arc
UniProt
Find proteins for Q63053 (Rattus norvegicus)
Explore Q63053 
Go to UniProtKB:  Q63053
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63053
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II SUBUNIT ALPHA7Mus musculusMutation(s): 0 
Gene Names: CAMK2A
EC: 2.7.11.17
UniProt
Find proteins for P11798 (Mus musculus)
Explore P11798 
Go to UniProtKB:  P11798
Entity Groups  
UniProt GroupP11798
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.527α = 90
b = 51.527β = 90
c = 69.929γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Data collection, Database references, Source and taxonomy, Structure summary