6Y4P

Calmodulin N53I variant bound to cardiac ryanodine receptor (RyR2) calmodulin binding domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The arrhythmogenic N53I variant subtly changes the structure and dynamics in the calmodulin N-terminal domain, altering its interaction with the cardiac ryanodine receptor.

Holt, C.Hamborg, L.Lau, K.Brohus, M.Sorensen, A.B.Larsen, K.T.Sommer, C.Van Petegem, F.Overgaard, M.T.Wimmer, R.

(2020) J Biol Chem 295: 7620-7634

  • DOI: https://doi.org/10.1074/jbc.RA120.013430
  • Primary Citation of Related Structures:  
    6Y4O, 6Y4P, 6Y94, 6Y95

  • PubMed Abstract: 

    Mutations in the genes encoding the highly conserved Ca 2+ -sensing protein calmodulin (CaM) cause severe cardiac arrhythmias, including catecholaminergic polymorphic ventricular tachycardia or long QT syndrome and sudden cardiac death. Most of the identified arrhythmogenic mutations reside in the C-terminal domain of CaM and mostly affect Ca 2+ -coordinating residues. One exception is the catecholaminergic polymorphic ventricular tachycardia-causing N53I substitution, which resides in the N-terminal domain (N-domain). It does not affect Ca 2+ coordination and has only a minor impact on binding affinity toward Ca 2+ and on other biophysical properties. Nevertheless, the N53I substitution dramatically affects CaM's ability to reduce the open probability of the cardiac ryanodine receptor (RyR2) while having no effect on the regulation of the plasmalemmal voltage-gated Ca 2+ channel, Ca v 1.2. To gain more insight into the molecular disease mechanism of this mutant, we used NMR to investigate the structures and dynamics of both apo- and Ca 2+ -bound CaM-N53I in solution. We also solved the crystal structures of WT and N53I CaM in complex with the primary calmodulin-binding domain (CaMBD2) from RyR2 at 1.84-2.13 Å resolutions. We found that all structures of the arrhythmogenic CaM-N53I variant are highly similar to those of WT CaM. However, we noted that the N53I substitution exposes an additional hydrophobic surface and that the intramolecular dynamics of the protein are significantly altered such that they destabilize the CaM N-domain. We conclude that the N53I-induced changes alter the interaction of the CaM N-domain with RyR2 and thereby likely cause the arrhythmogenic phenotype of this mutation.


  • Organizational Affiliation

    Aalborg University, Department of Chemistry and Bioscience, 9220 Aalborg, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin-1149Homo sapiensMutation(s): 1 
Gene Names: CALM1CALMCAMCAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
PHAROS:  P0DP23
GTEx:  ENSG00000198668 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP23
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ryanodine receptor 230Mus musculusMutation(s): 0 
Gene Names: Ryr2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92736 (Homo sapiens)
Explore Q92736 
Go to UniProtKB:  Q92736
PHAROS:  Q92736
GTEx:  ENSG00000198626 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92736
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.59α = 90
b = 42.36β = 90
c = 90.36γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Danish Council for Independent ResearchDenmarkDFF-1323-00344
Novo Nordisk FoundationDenmarkNNF18OC0053032
European Union (EU)Germany261863
Canadian Institutes of Health Research (CIHR)CanadaPJT-148632

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references
  • Version 1.2: 2020-06-10
    Changes: Database references
  • Version 1.3: 2020-07-29
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2024-01-24
    Changes: Data collection, Database references, Refinement description