8X4D

Cryo-EM structure of Ryanodine receptor 1 (TM helix S0,20 uM Ca2+, 2 mM ATP)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into transmembrane helix S0 facilitated RyR1 channel gating by Ca 2+ /ATP.

Wei, R.Chen, Q.Zhang, L.Liu, C.Liu, C.Yin, C.C.Hu, H.

(2025) Nat Commun 16: 1936-1936

  • DOI: https://doi.org/10.1038/s41467-025-57074-4
  • Primary Citation of Related Structures:  
    8X48, 8X49, 8X4A, 8X4B, 8X4C, 8X4D, 8X4E

  • PubMed Abstract: 

    The type-1 ryanodine receptor (RyR1) is an intracellular calcium release channel for skeletal muscle excitation-contraction coupling. Previous structural studies showed that the RyR1 activity is modulated by the exogenous regulators including caffeine, ryanodine, PCB-95 and diamide. An additional transmembrane helix, located adjacent to S1 and S4, has been observed in some structures, although its function remains unclear. Here, we report that using a mild purification procedure, this helix is co-purified with RyR1 and is designated as S0. When RyR1 is coupled with S0, it can be activated by Ca 2+ to an open state; however when decoupled from S0, it remains in primed state. S0 regulates the channel conformation by directly affecting the TM domain via the pVSD-S0-S4/S5 linker coupling, which facilitates the dilation of S6. Our results demonstrate that S0 is an essential component of RyR1 and plays a key role in the physiological regulation of RyR1 channel gating.


  • Organizational Affiliation

    Department of Biophysics, School of Basic Medical Sciences, Peking University, Beijing, 100191, China.


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 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2017YFA0504700
National Natural Science Foundation of China (NSFC)China31770785
National Natural Science Foundation of China (NSFC)China31900868
National Natural Science Foundation of China (NSFC)China32100963

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-03-12
    Changes: Data collection, Database references