6TNQ

Crystal structure of the human Arc N-lobe bound to repeat 4 from GKAP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.132 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural properties and peptide ligand binding of the capsid homology domains of human Arc.

Hallin, E.I.Bramham, C.R.Kursula, P.

(2021) Biochem Biophys Rep 26: 100975-100975

  • DOI: https://doi.org/10.1016/j.bbrep.2021.100975
  • Primary Citation of Related Structures:  
    6TN7, 6TNO, 6TNQ, 6TQ0

  • PubMed Abstract: 

    The activity-regulated cytoskeleton-associated protein (Arc) is important for synaptic plasticity and the normal function of the brain. Arc interacts with neuronal postsynaptic proteins, but the mechanistic details of its function have not been fully established. The C-terminal domain of Arc consists of tandem domains, termed the N- and C-lobe. The N-lobe harbours a peptide binding site, able to bind multiple targets. By measuring the affinity of human Arc towards various peptides from stargazin and guanylate kinase-associated protein (GKAP), we have refined its specificity determinants. We found two sites in the GKAP repeat region that bind to Arc and confirmed these interactions by X-ray crystallography. Phosphorylation of the stargazin peptide did not affect binding affinity but caused changes in thermodynamic parameters. Comparison of the crystal structures of three high-resolution human Arc-peptide complexes identifies three conserved C-H…π interactions at the binding cavity, explaining the sequence specificity of short linear motif binding by Arc. We further characterise central residues of the Arc lobe fold, show the effects of peptide binding on protein dynamics, and identify acyl carrier proteins as structures similar to the Arc lobes. We hypothesise that Arc may affect protein-protein interactions and phase separation at the postsynaptic density, affecting protein turnover and re-modelling of the synapse. The present data on Arc structure and ligand binding will help in further deciphering these processes.


  • 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, C, E
75Homo sapiensMutation(s): 0 
Gene Names: ARCKIAA0278
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

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Chains: B,D,F
B, D, F
8Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O14490 (Homo sapiens)
Explore O14490 
Go to UniProtKB:  O14490
PHAROS:  O14490
GTEx:  ENSG00000170579 
Entity Groups  
UniProt GroupO14490
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACE
Query on ACE

Download Ideal Coordinates CCD File 
G [auth D]ACETYL GROUP
C2 H4 O
IKHGUXGNUITLKF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.132 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.8α = 90
b = 29.37β = 93.4
c = 71.36γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Norwegian Research CouncilNorway249951

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-04-07
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description