6WOU

Cryo-EM structure of recombinant mouse Ryanodine Receptor type 2 mutant R176Q in complex with FKBP12.6 in nanodisc


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural mechanism of two gain-of-function cardiac and skeletal RyR mutations at an equivalent site by cryo-EM.

Iyer, K.A.Hu, Y.Nayak, A.R.Kurebayashi, N.Murayama, T.Samso, M.

(2020) Sci Adv 6: eabb2964-eabb2964

  • DOI: https://doi.org/10.1126/sciadv.abb2964
  • Primary Citation of Related Structures:  
    6WOT, 6WOU, 6WOV

  • PubMed Abstract: 

    Mutations in ryanodine receptors (RyRs), intracellular Ca 2+ channels, are associated with deadly disorders. Despite abundant functional studies, the molecular mechanism of RyR malfunction remains elusive. We studied two single-point mutations at an equivalent site in the skeletal (RyR1 R164C) and cardiac (RyR2 R176Q) isoforms using ryanodine binding, Ca 2+ imaging, and cryo-electron microscopy (cryo-EM) of the full-length protein. Loss of the positive charge had greater effect on the skeletal isoform, mediated via distortion of a salt bridge network, a molecular latch inducing rotation of a cytoplasmic domain, and partial progression to open-state traits of the large cytoplasmic assembly accompanied by alteration of the Ca 2+ binding site, which concur with the major "hyperactive" feature of the mutated channel. Our cryo-EM studies demonstrated the allosteric effect of a mutation situated ~85 Å away from the pore and identified an isoform-specific structural effect.


  • Organizational Affiliation

    Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ryanodine receptor 2
A, B, C, D
4,966Mus musculusMutation(s): 1 
Gene Names: Ryr2
Membrane Entity: Yes 
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP1B
E, F, G, H
107Homo sapiensMutation(s): 0 
Gene Names: FKBP1BFKBP12.6FKBP1LFKBP9OTK4
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P68106 (Homo sapiens)
Explore P68106 
Go to UniProtKB:  P68106
PHAROS:  P68106
GTEx:  ENSG00000119782 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68106
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC2.11

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United StatesR01 AR068431
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01 HL133182
Other privateUnited StatesMDA 352845
American Heart AssociationUnited States19POST34430178
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesHSSN26120080001E
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24 GM116789
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24 GM116790

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2021-03-31
    Changes: Structure summary
  • Version 1.2: 2022-08-03
    Changes: Database references
  • Version 1.3: 2024-05-29
    Changes: Data collection, Refinement description