9E1C | pdb_00009e1c

Structure of RyR1 in the primed state in the presence of IBMX


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.63 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Targeting ryanodine receptors with allopurinol and xanthine derivatives for the treatment of cardiac and musculoskeletal weakness disorders.

Miotto, M.C.Luna-Figueroa, E.Tchagou, C.Bahlouli, L.Reiken, S.Dridi, H.Liu, Y.Weninger, G.Marks, A.R.

(2025) Proc Natl Acad Sci U S A 122: e2422082122-e2422082122

  • DOI: https://doi.org/10.1073/pnas.2422082122
  • Primary Citation of Related Structures:  
    9E17, 9E18, 9E19, 9E1A, 9E1B, 9E1C, 9E1D, 9E1E, 9E1F, 9E1G, 9E1H, 9E1I

  • PubMed Abstract: 

    Ryanodine receptors (RyRs) are intracellular Ca 2+ channels essential for muscle contraction. Caffeine, a xanthine derivative, has been known for decades to increase muscle contraction and enhance activation of RyRs by increasing the sensitivity to Ca 2+ . We previously showed that xanthine, the only physiologically relevant xanthine derivative, also binds to and activates RyR2. Most xanthine derivatives and analogs are safe and widely prescribed, with the most popular being the xanthine oxidoreductase inhibitor allopurinol (~15M yearly prescriptions in USA). We propose that xanthine derivatives and analogs that enhance RyRs activity could be used for lead optimization and eventually for the treatment of the diseases that exhibit decreased muscle contraction and reduced RyRs activity, such as RyR1-related diseases, sarcopenia, and heart failure. Here, we show by cryo-EM that xanthine derivatives, analogs, and other related compounds bind to the xanthine/caffeine binding site and activate RyR1, and identify 4-oxopyrimidine as the minimal motif necessary for such interaction.


  • Organizational Affiliation
    • Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ryanodine receptor 1A,
F [auth B],
G [auth D],
H [auth C]
5,037Oryctolagus cuniculusMutation(s): 0 
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:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP1AB [auth E],
C [auth H],
D [auth G],
E [auth F]
108Oryctolagus cuniculusMutation(s): 0 
EC: 5.2.1.8
UniProt
Find proteins for P62943 (Oryctolagus cuniculus)
Explore P62943 
Go to UniProtKB:  P62943
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62943
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
I [auth A],
M [auth B],
Q [auth D],
U [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
IBM (Subject of Investigation/LOI)
Query on IBM

Download Ideal Coordinates CCD File 
L [auth A],
P [auth B],
T [auth D],
X [auth C]
3-ISOBUTYL-1-METHYLXANTHINE
C10 H14 N4 O2
APIXJSLKIYYUKG-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
K [auth A],
O [auth B],
S [auth D],
W [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
J [auth A],
N [auth B],
R [auth D],
V [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.63 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection
  • Version 1.2: 2025-06-25
    Changes: Data collection, Database references