9L90 | pdb_00009l90

The crystal structure of human RyR3 Repeat12 domain in complex with Dantrolene and AMP-PCP

• PDB DOI: https://doi.org/10.2210/pdb9L90/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-12-28 Released: 2025-10-22 
• Deposition Author(s): Hadiatullah, H., Lin, L., Yuchi, Z.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 
  0.319 (Depositor), 0.319 (DCC) 
• R-Value Work: 
  0.272 (Depositor), 0.274 (DCC) 

Starting Model: experimental

Literature

Structural Basis for the Modulation of Ryanodine Receptor by Dantrolene and Azumolene

Hadiatullah, H., Lin, L., Yuchi, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 101.61 kDa 
• Atom Count: 5,817 
• Modeled Residue Count: 801 
• Deposited Residue Count: 872 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor 3	A, B, C, D	218	Homo sapiens	Mutation(s): 0  Gene Names: RYR3, HBRR
UniProt & NIH Common Fund Data Resources
Find proteins for Q15413 (Homo sapiens) Explore Q15413  Go to UniProtKB:  Q15413
PHAROS:  Q15413 GTEx:  ENSG00000198838

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACP (Subject of Investigation/LOI)	F [auth A], H [auth B]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
U1C (Subject of Investigation/LOI)	E [auth A], G [auth B]	Dantrolene C14 H10 N4 O5 OZOMQRBLCMDCEG-CHHVJCJISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free:  0.319 (Depositor), 0.319 (DCC) 
• R-Value Work:  0.272 (Depositor), 0.274 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.739	α = 90
b = 60.839	β = 90
c = 262.52	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Hadiatullah, H., Lin, L., Yuchi, Z.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release