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- PDB-9l9b: The crystal structure of human RyR3 Repeat12 domain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 9l9b
TitleThe crystal structure of human RyR3 Repeat12 domain in complex with Dantrolene and ADP
ComponentsRyanodine receptor 3
KeywordsMEMBRANE PROTEIN / Repeat12 domain / dantranlene / ADP / ryanodine receptor
Function / homology
Function and homology information


calcium-induced calcium release activity / cellular response to magnesium ion / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cellular response to caffeine / cellular response to ATP / intracellularly gated calcium channel activity / smooth endoplasmic reticulum / Ion homeostasis / release of sequestered calcium ion into cytosol ...calcium-induced calcium release activity / cellular response to magnesium ion / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cellular response to caffeine / cellular response to ATP / intracellularly gated calcium channel activity / smooth endoplasmic reticulum / Ion homeostasis / release of sequestered calcium ion into cytosol / calcium channel complex / sarcoplasmic reticulum membrane / cellular response to calcium ion / sarcolemma / calcium ion transmembrane transport / Stimuli-sensing channels / Z disc / intracellular calcium ion homeostasis / calcium ion transport / protein homotetramerization / calmodulin binding / calcium ion binding / membrane
Similarity search - Function
Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain ...Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain / RyR/IP3 receptor binding core, RIH domain superfamily / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / : / MIR motif / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / Ryanodine receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsHadiatullah, H. / Lin, L. / Yuchi, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural Basis for the Modulation of Ryanodine Receptor by Dantrolene and Azumolene
Authors: Hadiatullah, H. / Lin, L. / Yuchi, Z.
History
DepositionDec 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Ryanodine receptor 3
D: Ryanodine receptor 3
C: Ryanodine receptor 3
A: Ryanodine receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4578
Polymers99,9744
Non-polymers1,4834
Water28816
1
B: Ryanodine receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7353
Polymers24,9941
Non-polymers7412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13160 Å2
MethodPISA
2
D: Ryanodine receptor 3


Theoretical massNumber of molelcules
Total (without water)24,9941
Polymers24,9941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13310 Å2
MethodPISA
3
C: Ryanodine receptor 3


Theoretical massNumber of molelcules
Total (without water)24,9941
Polymers24,9941
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13010 Å2
MethodPISA
4
A: Ryanodine receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7353
Polymers24,9941
Non-polymers7412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-4 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.043, 61.855, 279.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Ryanodine receptor 3 / RYR-3 / RyR3 / Brain ryanodine receptor-calcium release channel / Brain-type ryanodine receptor / ...RYR-3 / RyR3 / Brain ryanodine receptor-calcium release channel / Brain-type ryanodine receptor / Type 3 ryanodine receptor


Mass: 24993.588 Da / Num. of mol.: 4 / Fragment: Repeat12 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RYR3, HBRR
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q15413
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-U1C / Dantrolene / 1-[(Z)-{[5-(4-nitrophenyl)furan-2-yl]methylidene}amino]imidazolidine-2,4-dione


Mass: 314.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H10N4O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.6M sodium acetate trihydrate, 18% PEG 3350

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Data collection

DiffractionMean temperature: 297 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.8→144.03 Å / Num. obs: 26792 / % possible obs: 98.8 % / Redundancy: 9.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.079 / Rrim(I) all: 0.203 / Χ2: 1.03 / Net I/σ(I): 8.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.789 / Num. unique obs: 3841 / CC1/2: 0.657 / Rpim(I) all: 0.34 / Rrim(I) all: 0.898 / Χ2: 0.68

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
HKL-2000data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→139.6 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.315 --
obs0.281 25119 95.43 %
Refinement stepCycle: LAST / Resolution: 2.84→139.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5687 0 100 16 5803

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