6FOO

Structure of Ryanodine Receptor 1 in nanodiscs in the presence of calcium and ATP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Influence of Lipid Mimetics on Gating of Ryanodine Receptor.

Willegems, K.Efremov, R.G.

(2018) Structure 26: 1303-1313.e4

  • DOI: https://doi.org/10.1016/j.str.2018.06.010
  • Primary Citation of Related Structures:  
    6FG3, 6FOO

  • PubMed Abstract: 

    Understanding gating principles of ion channels at high resolution is of great importance. Here we investigate the conformational transition from closed to open state in ryanodine receptor 1 (RyR1) reconstituted into lipid nanodiscs. RyR1 is a homotetrameric giant ion channel that couples excitation of muscle cells to fast calcium release from the sarcoplasmic reticulum. Using single-particle cryo-EM we show that RyR1 reconstituted into lipid nanodiscs is stabilized in the open conformation when bound to the plant toxin ryanodine, but not in the presence of its physiological activators, calcium and ATP. Further, using ryanodine binding assays we show that membrane mimetics influence RyR1 transition between closed and open-channel conformations. We find that all detergents, including fluorinated detergents added to nanodiscs, stabilize closed state of RyR1. Our biochemical results correlate with available structural data and suggest optimal conditions for structural studies of RyR1 gating.


  • Organizational Affiliation

    Center for Structural Biology, Vlaams Instituut voor Biotechnologie, 1050 Brussels, Belgium; Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ryanodine receptor 1
A, B, C, D
5,037Oryctolagus cuniculusMutation(s): 0 
Membrane Entity: Yes 
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: ELECTRON MICROSCOPY
  • Resolution: 8.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIX1.12

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
IWTBelgium131261
FWOBelgiumG.0266.15N

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-08-15
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2018-08-29
    Changes: Data collection, Database references
  • Version 1.3: 2018-10-10
    Changes: Data collection, Database references, Structure summary
  • Version 1.4: 2018-11-28
    Changes: Data collection, Database references, Structure summary
  • Version 1.5: 2019-11-06
    Changes: Data collection, Refinement description