4P9J

Crystal Structure of rabbit Ryanodine Receptor 1 SPRY2 Domain (1070-1246)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structures of wild type and disease mutant forms of the ryanodine receptor SPRY2 domain.

Lau, K.Van Petegem, F.

(2014) Nat Commun 5: 5397-5397

  • DOI: https://doi.org/10.1038/ncomms6397
  • Primary Citation of Related Structures:  
    4P9I, 4P9J, 4P9L

  • PubMed Abstract: 

    Ryanodine receptors (RyRs) form channels responsible for the release of Ca(2+) from the endoplasmic and sarcoplasmic reticulum. The SPRY2 domain in the skeletal muscle isoform (RyR1) has been proposed as a direct link with L-type calcium channels (CaV1.1), allowing for direct mechanical coupling between plasma membrane depolarization and Ca(2+) release. Here we present the crystal structures of the SPRY2 domain from RyR1 and RyR2 at 1.34-1.84 Å resolution. They form two antiparallel β sheets establishing a core, and four additional modules of which several are required for proper folding. A buried disease mutation, linked to hypertrophic cardiomyopathy and loss-of-function, induces local misfolding and strong destabilization. Isothermal titration calorimetry experiments negate the RyR1 SPRY2 domain as the major link with CaV1.1. Instead, docking into full-length RyR1 cryo-electron microscopy maps suggests that the SPRY2 domain forms a link between the N-terminal gating ring and the clamp region.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ryanodine receptor 1A [auth C],
B [auth A],
C [auth B]
180Oryctolagus cuniculusMutation(s): 0 
Gene Names: RYR1
UniProt
Find proteins for P11716 (Oryctolagus cuniculus)
Explore P11716 
Go to UniProtKB:  P11716
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11716
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.58α = 89.97
b = 37.57β = 89.97
c = 95.82γ = 120.05
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.2: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Refinement description