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
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Ligand Structure Quality Assessment

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Literature

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

Hadiatullah, H., Lin, L., Yuchi, Z.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15413
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACP (Subject of Investigation/LOI) Query on ACP Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B]
U1C (Subject of Investigation/LOI) Query on U1C Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	E [auth A], G [auth B]	Dantrolene C₁₄ H₁₀ N₄ O₅ OZOMQRBLCMDCEG-CHHVJCJISA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

Hadiatullah, H.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.