Crystal structure of Ca2+/Calmodulin complexed with myristoylated CAP-23/NAP-22 peptide

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.249 

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Crystal structure of a myristoylated CAP-23/NAP-22 N-terminal domain complexed with Ca2+/calmodulin

Matsubara, M.Nakatsu, T.Kato, H.Taniguchi, H.

(2004) EMBO J 23: 712-718

  • DOI: https://doi.org/10.1038/sj.emboj.7600093
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A variety of viral and signal transduction proteins are known to be myristoylated. Although the role of myristoylation in protein-lipid interaction is well established, the involvement of myristoylation in protein-protein interactions is less well understood. CAP-23/NAP-22 is a brain-specific protein kinase C substrate protein that is involved in axon regeneration. Although the protein lacks any canonical calmodulin (CaM)-binding domain, it binds CaM with high affinity. The binding of CAP-23/NAP-22 to CaM is myristoylation dependent and the N-terminal myristoyl group is directly involved in the protein-protein interaction. Here we show the crystal structure of Ca2+-CaM bound to a myristoylated peptide corresponding to the N-terminal domain of CAP-23/NAP-22. The myristoyl moiety of the peptide goes through a hydrophobic tunnel created by the hydrophobic pockets in the N- and C-terminal domains of CaM. In addition to the myristoyl group, several amino-acid residues in the peptide are important for CaM binding. This is a novel mode of binding and is very different from the mechanism of binding in other CaM-target complexes.

  • Organizational Affiliation

    Membrane Dynamics Project, Harima Institute at SPring-8, RIKEN, Sayo, Hyogo, Japan. mamoru.matsubara@carnabio.com

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CALMODULIN148Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
GTEx:  ENSG00000198668 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP23
Sequence Annotations
  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CAP-23/NAP-229N/AMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.249 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.6α = 90
b = 40.6β = 90
c = 173.639γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-16
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description