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- PDB-9l90: The crystal structure of human RyR3 Repeat12 domain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 9l90
TitleThe crystal structure of human RyR3 Repeat12 domain in complex with Dantrolene and AMP-PCP
ComponentsRyanodine receptor 3
KeywordsMEMBRANE PROTEIN / Repeat12 domain / dantranlene / AMP-PCP / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / : / Ryanodine receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 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 28, 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
A: Ryanodine receptor 3
B: Ryanodine receptor 3
C: Ryanodine receptor 3
D: Ryanodine receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6138
Polymers99,9744
Non-polymers1,6394
Water27015
1
A: Ryanodine receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8133
Polymers24,9941
Non-polymers8192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-0 kcal/mol
Surface area11510 Å2
MethodPISA
2
B: Ryanodine receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8133
Polymers24,9941
Non-polymers8192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-3 kcal/mol
Surface area11470 Å2
MethodPISA
3
C: 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 area11820 Å2
MethodPISA
4
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 area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.739, 60.839, 262.520
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-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
#3: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.7M sodium acetate trihydrate, 14% 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: 2.79→131.26 Å / Num. obs: 25177 / % possible obs: 99.3 % / Redundancy: 6.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.026 / Rrim(I) all: 0.061 / Χ2: 1.09 / Net I/σ(I): 13.2 / Num. measured all: 304066
Reflection shellResolution: 2.79→2.94 Å / % possible obs: 99.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.821 / Num. measured all: 45462 / Num. unique obs: 3580 / CC1/2: 0.792 / Rpim(I) all: 0.209 / Rrim(I) all: 0.851 / Χ2: 0.8 / Net I/σ(I) obs: 3.8

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.14refinement
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→131.26 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.319 --
Rwork0.272 --
obs-25119 99.76 %
Refinement stepCycle: LAST / Resolution: 2.79→131.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5694 0 108 15 5817
LS refinement shellResolution: 2.79→2.89 Å
RfactorNum. reflection% reflection
Rfree0.403 --
Rwork0.332 --
obs-2487 99.96 %

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