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- PDB-4l4h: Crystal structure of mouse Ryanodine Receptor isoform 2 (RyR2) 1-547 -

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Basic information

Entry
Database: PDB / ID: 4l4h
TitleCrystal structure of mouse Ryanodine Receptor isoform 2 (RyR2) 1-547
ComponentsRyanodine receptor 2
KeywordsMETAL TRANSPORT / Ca2+ release / ion channel / ER/SR Membrane
Function / homology
Function and homology information


manganese ion transmembrane transport / suramin binding / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / 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 / suramin binding / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / 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 / ventricular cardiac muscle cell action potential / regulation of 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 / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to muscle activity / calcium ion transport into cytosol / response to caffeine / A band / response to redox state / calcium ion transmembrane import into cytosol / positive regulation of heart rate / negative regulation of cytosolic calcium ion concentration / cellular response to caffeine / protein kinase A regulatory subunit binding / intracellularly gated calcium channel activity / protein kinase A catalytic subunit binding / positive regulation of the force of heart contraction / extrinsic component of cytoplasmic side of plasma membrane / 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 / monoatomic ion transmembrane transport / regulation of cytosolic calcium ion concentration / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to epinephrine stimulus / response to muscle stretch / regulation of heart rate / sarcomere / sarcoplasmic reticulum / establishment of localization in cell / calcium ion transmembrane transport / calcium-mediated signaling / response to calcium ion / calcium channel activity / sarcolemma / Z disc / intracellular calcium ion homeostasis / nuclear envelope / calcium ion 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
IP3 receptor type 1 binding core, RIH domain / : / Ryanodine receptor junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / 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 ...IP3 receptor type 1 binding core, RIH domain / : / Ryanodine receptor junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / 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. / Leucine-rich Repeat Variant / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / 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 / Alpha Horseshoe / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Ryanodine receptor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKimlicka, L. / Tung, C.C. / Van Petegem, F.
CitationJournal: To be Published
Title: Crystal structure of a ryanodine receptor domain
Authors: Kimlicka, L. / Tung, C.C. / Carlsson, A.C. / Lobo, P.A. / Van Petegem, F.
History
DepositionJun 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ryanodine receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8704
Polymers61,5791
Non-polymers2923
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.040, 78.040, 248.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Ryanodine receptor 2 / RYR-2 / RyR2 / Cardiac muscle ryanodine receptor / Cardiac muscle ryanodine receptor-calcium ...RYR-2 / RyR2 / Cardiac muscle ryanodine receptor / Cardiac muscle ryanodine receptor-calcium release channel / Type 2 ryanodine receptor / Cardiac Ca2+ release channel


Mass: 61578.637 Da / Num. of mol.: 1 / Fragment: N-terminal domains (UNP residues 1-547)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ryr2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: E9Q401
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 3.07 Å3/Da / Density % sol: 59.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.15
Details: 6% PEG3350, 0.1 M Tris, pH 8.15, 0.8% ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 23, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 53023 / Num. obs: 52836 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.091 / Rsym value: 0.156
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.055.81.7321.99199.9
2.05-2.11199.9
2.11-2.171100
2.17-2.241100
2.24-2.31199.9
2.31-2.391100
2.39-2.481100
2.48-2.581100
2.58-2.71100
2.7-2.831100
2.83-2.981100
2.98-3.161100
3.16-3.381100
3.38-3.65199.9
3.65-4199.7
4-4.47199.6
4.47-5.16199.2
5.16-6.32197.8
6.32-8.94183.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0110refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XOA

2xoa


Resolution: 2→48.71 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25108 2645 5 %RANDOM
Rwork0.22026 ---
obs0.2218 50190 100 %-
all-53023 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.648 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20 Å2
2--1.21 Å20 Å2
3----2.43 Å2
Refinement stepCycle: LAST / Resolution: 2→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3538 0 18 82 3638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0213653
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8091.9444953
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5575469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59322.975158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.50815573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5131526
X-RAY DIFFRACTIONr_chiral_restr0.1420.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022746
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_it1.1921.52313
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.09523661
X-RAY DIFFRACTIONr_scbond_it3.12131340
X-RAY DIFFRACTIONr_scangle_it4.6844.51287
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 197 -
Rwork0.293 3659 -
obs--99.95 %
Refinement TLS params.

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)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.3506-1.20920.38862.34670.44184.3550.30860.50910.0936-0.0407-0.1677-0.26290.0479-0.1053-0.1410.07550.0744-0.02730.14880.06130.2168-7.06417.14649.565
22.87-0.6624-0.97421.97850.13724.25840.04310.0461-0.1514-0.2705-0.0863-0.03330.47770.65370.04310.17180.19860.03080.30850.03380.1384-14.48316.81118.17
32.18080.0046-1.17210.93930.16143.3901-0.0158-0.08020.11070.06510.02790.01480.23030.0777-0.01220.05870.0617-0.00350.0960.01280.1844-33.5529.69739.664
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 217
2X-RAY DIFFRACTION2A218 - 409
3X-RAY DIFFRACTION3A410 - 543

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