6J6L

Crystal structure of mouse Ryanodine Receptor 2 SPRY1 Domain (650-844) disease mutant I784F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A SPRY1 domain cardiac ryanodine receptor variant associated with short-coupled torsade de pointes.

Touat-Hamici, Z.Blancard, M.Ma, R.Lin, L.Iddir, Y.Denjoy, I.Leenhardt, A.Yuchi, Z.Guicheney, P.

(2021) Sci Rep 11: 5243-5243

  • DOI: https://doi.org/10.1038/s41598-021-84373-9
  • Primary Citation of Related Structures:  
    6J6L

  • PubMed Abstract: 

    Idiopathic ventricular fibrillation (IVF) causes sudden death in young adult patients without structural or ischemic heart disease. Most IVF cases are sporadic and some patients present with short-coupled torsade de pointes, the genetics of which are poorly understood. A man who had a first syncope at the age of 35 presented with frequent short-coupled premature ventricular beats with bursts of polymorphic ventricular tachycardia and then died suddenly. By exome sequencing, we identified three rare variants: p.I784F in the SPRY1 of the ryanodine receptor 2 (RyR2), p.A96S in connexin 40 (Cx40), reported to affect electrical coupling and cardiac conduction, and a nonsense p.R244X in the cardiac-specific troponin I-interacting kinase (TNNI3K). We assessed intracellular Ca 2+ handling in WT and mutant human RYR2 transfected HEK293 cells by fluorescent microscopy and an enhanced store overload-induced Ca 2+ release in response to cytosolic Ca 2+ was observed in RyR2-I784F cells. In addition, crystal structures and thermal melting temperatures revealed a conformational change in the I784F-SPRY1 domain compared to the WT-domain. The novel RyR2-I784F variant in SPRY1 domain causes a leaky channel under non-stress conditions. The presence of several variants affecting Ca 2+ handling and cardiac conduction suggests a possible oligogenic origin for the ectopies originating from Purkinje fibres.


  • Organizational Affiliation

    INSERM, UMRS 1166, Faculté de Médecine Sorbonne-Université, Unité de Recherche sur les Maladies Cardiovasculaires et Métaboliques, 91, boulevard de l'Hôpital, 75013, Paris, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ryanodine receptor 2
A, B
198Mus 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: 1.45 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.945α = 90
b = 64.375β = 90
c = 108.48γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description