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- PDB-3im5: Crystal structure of mouse Ryanodine Receptor 2 (residues 1-217) -

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Basic information

Entry
Database: PDB / ID: 3im5
TitleCrystal structure of mouse Ryanodine Receptor 2 (residues 1-217)
ComponentsCardiac Ca2+ release channel
KeywordsSIGNALING PROTEIN / ryanodine receptor 2 / calcium release channel / cardiac channel / ion channel / ARVC2 / ARVD2 / CPVT / cardiac arrhythmia / Ion transport / Ionic channel / Transmembrane / Transport
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 / calcium ion transport into cytosol / ryanodine-sensitive calcium-release channel activity / response to caffeine / response to muscle activity / A band / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / calcium ion transmembrane import into cytosol / response to redox state / positive regulation of heart rate / negative regulation of cytosolic calcium ion concentration / protein kinase A regulatory subunit binding / extrinsic component of cytoplasmic side of plasma membrane / cellular response to caffeine / protein kinase A catalytic subunit binding / response to magnesium ion / positive regulation of the force of heart contraction / intracellularly gated calcium channel activity / 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 / sarcoplasmic reticulum membrane / response to muscle stretch / 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 / response to hypoxia / calmodulin binding / calcium ion binding / protein kinase binding / enzyme binding / protein-containing complex / identical protein 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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / EF-hand domain pair / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
Ryanodine receptor 2 / Ryanodine receptor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsVan Petegem, F. / Lobo, P.A.
CitationJournal: Structure / Year: 2009
Title: Crystal structures of the N-terminal domains of cardiac and skeletal muscle ryanodine receptors: insights into disease mutations.
Authors: Lobo, P.A. / Van Petegem, F.
History
DepositionAug 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cardiac Ca2+ release channel
B: Cardiac Ca2+ release channel


Theoretical massNumber of molelcules
Total (without water)48,3342
Polymers48,3342
Non-polymers00
Water61334
1
A: Cardiac Ca2+ release channel


Theoretical massNumber of molelcules
Total (without water)24,1671
Polymers24,1671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cardiac Ca2+ release channel


Theoretical massNumber of molelcules
Total (without water)24,1671
Polymers24,1671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)154.971, 39.030, 107.623
Angle α, β, γ (deg.)90.00, 131.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cardiac Ca2+ release channel


Mass: 24167.201 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ryr2 / Plasmid: pET28HMT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 pLacI / References: UniProt: Q9ERN6, UniProt: E9Q401*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.5-1.5M sodium malonate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 13, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.55→80.32 Å / Num. all: 15222 / Num. obs: 15222 / % possible obs: 93.6 % / Redundancy: 3.4 % / Rsym value: 0.381 / Net I/σ(I): 19.2
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.382 / % possible all: 58.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RyR2 NTD V186M mutant

Resolution: 2.55→80.32 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.863 / SU B: 22.139 / SU ML: 0.219 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.49 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28777 761 5 %RANDOM
Rwork0.22128 ---
obs0.22458 14423 94.42 %-
all-14423 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.274 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å2-0.97 Å2
2---0.3 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.55→80.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2615 0 0 34 2649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212675
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.9423648
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1475346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.86624.057106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.45715408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.471513
X-RAY DIFFRACTIONr_chiral_restr0.0820.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021983
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5481.51731
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05922754
X-RAY DIFFRACTIONr_scbond_it1.3293944
X-RAY DIFFRACTIONr_scangle_it2.2224.5891
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 32 -
Rwork0.272 665 -
obs--59.57 %
Refinement TLS params.

T22: 0.135 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.51220.11540.46751.81920.14891.80530.01890.20460.0491-0.0376-0.0262-0.21540.0270.06350.00730.0508-0.00890.02260.02210.106822.548-18.00829.658
21.9280.2492-0.66132.3037-0.5273.0494-0.0493-0.02520.00420.0669-0.0109-0.11240.04270.07790.06030.0847-0.0122-0.0237-0.01960.050714.271-27.74360.201
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 217
2X-RAY DIFFRACTION2B1 - 217

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