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 1.2 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: 10.1074/jbc.RA120.013430
  • Structures With Same Primary Citation

  • 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 (CPVT) or long QT syndrome, and sudden cardiac d ...

    Mutations in the genes encoding the highly conserved Ca 2+ -sensing protein calmodulin (CaM) cause severe cardiac arrhythmias, including catecholaminergic polymorphic ventricular tachycardia (CPVT) 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 CPVT-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 insights 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 wild-type 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 wild type 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

    Biotechnology, Aalborg University, Denmark.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Calmodulin
A
149Homo sapiensMutation(s): 1 
Gene Names: CALM1CALMCAMCAM1
Find proteins for P0DP23 (Homo sapiens)
Go to UniProtKB:  P0DP23
NIH Common Fund Data Resources
PHAROS  P0DP23

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ryanodine receptor 2
B
30Loxodonta africanaMutation(s): 0 
Gene Names: RYR3
Find proteins for G3ULN8 (Loxodonta africana)
Go to UniProtKB:  G3ULN8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
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 

  • 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