5VSN | pdb_00005vsn

Crystal structure of mouse ryanodine receptor 2 SPRY2 domain (1080-1253) disease mutant P1124L


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 
    0.193 (Depositor), 0.193 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Cardiac hypertrophy and arrhythmia in mice induced by a mutation in ryanodine receptor 2.

Alvarado, F.J.Bos, J.M.Yuchi, Z.Valdivia, C.R.Hernandez, J.J.Zhao, Y.T.Henderlong, D.S.Chen, Y.Booher, T.R.Marcou, C.A.Van Petegem, F.Ackerman, M.J.Valdivia, H.H.

(2019) JCI Insight 5

  • DOI: https://doi.org/10.1172/jci.insight.126544
  • Primary Citation Related Structures: 
    5VSN

  • PubMed Abstract: 

    Hypertrophic cardiomyopathy (HCM) is triggered mainly by mutations in genes encoding sarcomeric proteins, but a significant proportion of patients lack a genetic diagnosis. We identified a novel mutation in the ryanodine receptor 2, RyR2-P1124L, in a patient from a genotype-negative HCM cohort. The aim of this study was to determine whether RyR2-P1124L triggers functional and structural alterations in isolated RyR2 channels and whole hearts. We found that P1124L induces significant conformational changes in the SPRY2 domain of RyR2. Recombinant RyR2-P1124L channels displayed a cytosolic loss-of-function phenotype, which contrasted with a higher sensitivity to luminal [Ca2+], indicating a luminal gain-of-function. Homozygous mice for RyR2-P1124L showed mild cardiac hypertrophy, similar to the human patient. This phenotype, evident at 1 yr of age, was accompanied by an increase in the expression of calmodulin (CaM). P1124L mice also showed higher susceptibility to arrhythmia at 8 mo of age, before the onset of hypertrophy. RyR2-P1124L has a distinct cytosolic loss-of-function and a luminal gain-of-function phenotype. This bifunctionally-divergent behavior triggers arrhythmias and structural cardiac remodeling, and involves overexpression of calmodulin as a potential hypertrophic mediator. This study is relevant to continue elucidating the possible causes of genotype-negative HCM and the role of RyR2 in cardiac hypertrophy.


  • Organizational Affiliation
    • Department of Medicine, Division of Cardiovascular Medicine, and Cardiovascular Research Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA.

Macromolecule Content 

  • Total Structure Weight: 19.3 kDa 
  • Atom Count: 1,518 
  • Modeled Residue Count: 169 
  • Deposited Residue Count: 169 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ryanodine receptor 2169Mus musculusMutation(s): 1 
Gene Names: Ryr2
UniProt & NIH Common Fund Data Resources
Find proteins for E9Q401 (Mus musculus)
Explore E9Q401 
Go to UniProtKB:  E9Q401
IMPC:  MGI:99685
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9Q401
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free:  0.193 (Depositor), 0.193 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.29α = 90
b = 66.23β = 90
c = 66.98γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
Cootmodel building
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description