9L9B | pdb_00009l9b

The crystal structure of human RyR3 Repeat12 domain in complex with Dantrolene and ADP

PDB DOI: https://doi.org/10.2210/pdb9L9B/pdb

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

Deposited: 2024-12-29 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: 2.84 Å
R-Value Free:
0.315 (Depositor), 0.322 (DCC)
R-Value Work:
0.280 (DCC)
R-Value Observed:
0.281 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9L9B

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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: 101.46 kDa
Atom Count: 5,803
Modeled Residue Count: 814
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 [auth B], B [auth D], C, D [auth A]	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
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain E [auth B] MOL2 format, chain G [auth A] MOL2 format, chain E [auth B] mmCIF format, chain G [auth A] mmCIF format, chain E [auth B]	E [auth B], G [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth B] Focus chain G [auth A] Interactions & Density Focus chain E [auth B] Focus chain G [auth A]
U1C (Subject of Investigation/LOI) Query on U1C Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain F [auth B] MOL2 format, chain H [auth A] MOL2 format, chain F [auth B] mmCIF format, chain H [auth A] mmCIF format, chain F [auth B]	F [auth B], H [auth A]	Dantrolene C₁₄ H₁₀ N₄ O₅ OZOMQRBLCMDCEG-CHHVJCJISA-N		Interactions Focus chain F [auth B] Focus chain H [auth A] Interactions & Density Focus chain F [auth B] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.84 Å
R-Value Free: 0.315 (Depositor), 0.322 (DCC)
R-Value Work: 0.280 (DCC)
R-Value Observed: 0.281 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.043	α = 90
b = 61.855	β = 90
c = 279.128	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.