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- PDB-5c33: Crystal Structure of Mouse Ryanodine Receptor 2 SPRY1 Domain -

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Basic information

Entry
Database: PDB / ID: 5c33
TitleCrystal Structure of Mouse Ryanodine Receptor 2 SPRY1 Domain
ComponentsRyanodine receptor 2
KeywordsCONTRACTILE PROTEIN / SPRY / ligand-binding
Function / homology
Function and homology information


manganese ion transmembrane transport / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / suramin binding / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis / organic cyclic compound binding / regulation of AV node cell action potential ...manganese ion transmembrane transport / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / suramin binding / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis / organic cyclic compound binding / regulation of AV node cell action potential / calcium-induced calcium release activity / sarcoplasmic reticulum calcium ion transport / Stimuli-sensing channels / Ion homeostasis / regulation of ventricular cardiac muscle cell action potential / ventricular cardiac muscle cell action potential / positive regulation of sequestering of calcium ion / embryonic heart tube morphogenesis / cardiac muscle hypertrophy / ryanodine-sensitive calcium-release channel activity / response to caffeine / calcium ion transport into cytosol / response to muscle activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / A band / response to redox state / calcium ion transmembrane import into cytosol / positive regulation of heart rate / negative regulation of cytosolic calcium ion concentration / protein kinase A regulatory subunit binding / cellular response to caffeine / extrinsic component of cytoplasmic side of plasma membrane / protein kinase A catalytic subunit binding / positive regulation of the force of heart contraction / intracellularly gated calcium channel activity / response to magnesium ion / detection of calcium ion / smooth endoplasmic reticulum / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / striated muscle contraction / regulation of cytosolic calcium ion concentration / calcium channel complex / cellular response to epinephrine stimulus / response to muscle stretch / sarcoplasmic reticulum membrane / regulation of heart rate / sarcomere / sarcoplasmic reticulum / establishment of localization in cell / calcium-mediated signaling / calcium ion transmembrane transport / calcium channel activity / sarcolemma / Z disc / response to calcium ion / intracellular calcium ion homeostasis / calcium ion transport / nuclear envelope / monoatomic ion transmembrane transport / scaffold protein binding / calmodulin binding / response to hypoxia / calcium ion binding / protein kinase binding / enzyme binding / protein-containing complex / identical protein binding / membrane
Similarity search - Function
SPRY 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 ...SPRY 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 pair / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Ryanodine receptor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.21 Å
AuthorsYuchi, Z. / Van Petegem, F.
Funding support Canada, United States, 3items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-119608 Canada
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R01AR059124 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL092097 United States
CitationJournal: Nat Commun / Year: 2015
Title: Crystal structures of ryanodine receptor SPRY1 and tandem-repeat domains reveal a critical FKBP12 binding determinant.
Authors: Yuchi, Z. / Yuen, S.M. / Lau, K. / Underhill, A.Q. / Cornea, R.L. / Fessenden, J.D. / Van Petegem, F.
History
DepositionJun 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ryanodine receptor 2
B: Ryanodine receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3375
Polymers44,1822
Non-polymers1563
Water8,629479
1
A: Ryanodine receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1863
Polymers22,0911
Non-polymers962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ryanodine receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1512
Polymers22,0911
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.246, 64.085, 109.769
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 2 / RyR2 / Cardiac muscle ryanodine receptor / Cardiac muscle ryanodine receptor-calcium release ...RyR2 / Cardiac muscle ryanodine receptor / Cardiac muscle ryanodine receptor-calcium release channel / Type 2 ryanodine receptor


Mass: 22090.803 Da / Num. of mol.: 2 / Fragment: SPRY1 domain (UNP residues 650-844)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ryr2 / Plasmid: pET28-HMT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta(DE3) / References: UniProt: E9Q401
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium acetate, pH 5.0, 0.6-0.9 M sodium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.975910, 0.979518, 1.377552
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 22, 2013
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.975911
20.9795181
31.3775521
ReflectionResolution: 1.21→38.371 Å / Num. obs: 114712 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 13.02 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 17.81
Reflection shellResolution: 1.21→1.25 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.915 / Mean I/σ(I) obs: 2.16 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.21→38.371 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1725 5741 5 %
Rwork0.1433 --
obs0.1447 114708 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.21→38.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2749 0 9 479 3237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153066
X-RAY DIFFRACTIONf_angle_d1.5944189
X-RAY DIFFRACTIONf_dihedral_angle_d12.4321082
X-RAY DIFFRACTIONf_chiral_restr0.124420
X-RAY DIFFRACTIONf_plane_restr0.009558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2105-1.22420.27581990.2563411X-RAY DIFFRACTION96
1.2242-1.23860.24481930.22263603X-RAY DIFFRACTION100
1.2386-1.25370.24271820.21163589X-RAY DIFFRACTION100
1.2537-1.26960.24472080.20443592X-RAY DIFFRACTION100
1.2696-1.28630.2261880.18733606X-RAY DIFFRACTION100
1.2863-1.30390.21561820.17763599X-RAY DIFFRACTION100
1.3039-1.32260.21681900.17643610X-RAY DIFFRACTION100
1.3226-1.34230.21212010.16273575X-RAY DIFFRACTION100
1.3423-1.36330.21271940.15163613X-RAY DIFFRACTION100
1.3633-1.38560.18491880.14813586X-RAY DIFFRACTION100
1.3856-1.40950.19411890.14423602X-RAY DIFFRACTION100
1.4095-1.43520.15931840.13753635X-RAY DIFFRACTION100
1.4352-1.46280.18711950.13033605X-RAY DIFFRACTION100
1.4628-1.49260.18511940.12863618X-RAY DIFFRACTION100
1.4926-1.52510.15972030.12063622X-RAY DIFFRACTION100
1.5251-1.56060.14991780.11723614X-RAY DIFFRACTION100
1.5606-1.59960.14981630.11323622X-RAY DIFFRACTION100
1.5996-1.64280.16222180.1153593X-RAY DIFFRACTION100
1.6428-1.69120.16171970.11563622X-RAY DIFFRACTION100
1.6912-1.74580.15122060.11583628X-RAY DIFFRACTION100
1.7458-1.80820.1522000.11553613X-RAY DIFFRACTION100
1.8082-1.88060.16081970.11943641X-RAY DIFFRACTION100
1.8806-1.96620.14581840.11713664X-RAY DIFFRACTION100
1.9662-2.06980.1511960.12333653X-RAY DIFFRACTION100
2.0698-2.19950.1361910.12343648X-RAY DIFFRACTION100
2.1995-2.36930.16531770.13143690X-RAY DIFFRACTION100
2.3693-2.60770.17561780.14333704X-RAY DIFFRACTION100
2.6077-2.98490.1831890.1463723X-RAY DIFFRACTION100
2.9849-3.76010.15911860.14243760X-RAY DIFFRACTION100
3.7601-38.390.19231910.17873926X-RAY DIFFRACTION100

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