9CGP | pdb_00009cgp

RyR1 disease mutant Y523S with FKBP12.6, nanodisc and inhibitor dantrolene in the absence of calcium with refined P1 domain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9CGP

This is version 1.2 of the entry. See complete history

Literature

Dantrolene inhibition of ryanodine receptor 1 carrying the severe malignant hyperthermia mutation Y522S visualized by cryo-EM.

Iyer, K.A.Kobayashi, T.Murayama, T.Samso, M.

(2025) Structure 33: 338-348.e4

  • DOI: https://doi.org/10.1016/j.str.2024.11.018
  • Primary Citation Related Structures: 
    9CGP

  • PubMed Abstract: 

    Mutations in the skeletal isoform of the ryanodine receptor 1 (RyR1) pose grave risks during anesthesia or treatment with succinylcholine muscle relaxants. These can trigger a potentially lethal malignant hyperthermia (MH) episode via intracellular calcium increase mainly from RyR1 channel leakage. Dantrolene is the only known treatment option to prevent death. The main target of dantrolene is RyR1; however, little is known about the mechanism of inhibition. Cryoelectron microscopy (cryo-EM) structures of dantrolene bound to the severe MH Y522S RyR1 mutant in the closed and open states at 2.5-3.3 Å resolution revealed that the drug binds to the channel's cytoplasmic assembly, far from the ion gate, interacting with residues W882, W996, and R1000 in the P1 domain. The finding was validated by Ca 2+ imaging and [ 3 H]ryanodine binding in wild-type (WT) and alanine mutants. Dantrolene reduced channel opening probability by restricting the central activation module, "cooling down" the primed conformation caused by the mutation.


  • Organizational Affiliation
    • Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA.

Macromolecule Content 

  • Total Structure Weight: 2,313.55 kDa 
  • Atom Count: 132,860 
  • Modeled Residue Count: 17,460 
  • Deposited Residue Count: 20,576 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ryanodine receptor 1
A, B, C, D
5,037Oryctolagus cuniculusMutation(s): 1 
Gene Names: RYR1
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
Find similar proteins by:|  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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
(Subject of Investigation/LOI)

Query on ATP



Download:Ideal Coordinates CCD File
J [auth A],
M [auth B],
P [auth C],
S [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
U1C
(Subject of Investigation/LOI)

Query on U1C



Download:Ideal Coordinates CCD File
K [auth A],
N [auth B],
Q [auth C],
T [auth D]
Dantrolene
C14 H10 N4 O5
OZOMQRBLCMDCEG-CHHVJCJISA-N
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
I [auth A],
L [auth B],
O [auth C],
R [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.1
MODEL REFINEMENTPHENIX20

Structure Validation

View Full Validation Report



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
American Heart AssociationUnited States19POST34430178
Other privateMDA 352845
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: 2024-12-11
    Type: Initial release
  • Version 1.1: 2025-02-05
    Changes: Data collection, Database references
  • Version 1.2: 2025-02-19
    Changes: Data collection, Database references