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- PDB-3qr5: Structure of the first domain of a cardiac Ryanodine Receptor mut... -

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Basic information

Entry
Database: PDB / ID: 3qr5
TitleStructure of the first domain of a cardiac Ryanodine Receptor mutant with exon 3 deleted
ComponentsCardiac Ca2+ release channel
KeywordsSIGNALING PROTEIN / beta trefoil / Sarcoplasmic reticulum
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 / calcium ion transmembrane import into cytosol / response to caffeine / A band / response to redox state / 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 / 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 / extrinsic component of cytoplasmic side of plasma membrane / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to epinephrine stimulus / regulation of cytosolic calcium ion concentration / 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 / intracellular calcium ion homeostasis / response to calcium ion / calcium ion transport / : / nuclear envelope / 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
: / 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 ...: / 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. / 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 / 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 / molecular replacement / Resolution: 2.3 Å
AuthorsLobo, P.A. / Van Petegem, F.
CitationJournal: Structure / Year: 2011
Title: The deletion of exon 3 in the cardiac ryanodine receptor is rescued by beta strand switching.
Authors: Lobo, P.A. / Kimlicka, L. / Tung, C.C. / Van Petegem, F.
History
DepositionFeb 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 26, 2023Group: Database references
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,2722
Polymers41,2722
Non-polymers00
Water75742
1
A: Cardiac Ca2+ release channel


Theoretical massNumber of molelcules
Total (without water)20,6361
Polymers20,6361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cardiac Ca2+ release channel


Theoretical massNumber of molelcules
Total (without water)20,6361
Polymers20,6361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.370, 44.204, 76.606
Angle α, β, γ (deg.)90.000, 90.980, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cardiac Ca2+ release channel


Mass: 20636.131 Da / Num. of mol.: 2
Fragment: RyR2A delta-Exon3 (UNP Residues 1-217 delta 57-91)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ryr2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ERN6, UniProt: E9Q401*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 1.96 Å3/Da / Density % sol: 37.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10-15% PEG 1000. Crystals frozen in 25% 2-methane-2,4-pentanediol cryoprotectant, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9729 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 30, 2009
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9729 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 14525 / Num. obs: 12917 / % possible obs: 84.5 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.065 / Χ2: 1.143 / Net I/σ(I): 14
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.381.30.29231.06132.9
2.38-2.481.40.18615301.15154.8
2.48-2.591.60.16320241.03173.4
2.59-2.731.70.15624851.137188.2
2.73-2.91.90.12326930.891197.4
2.9-3.121.90.09627821.109199.7
3.12-3.4420.08127891.268199.9
3.44-3.9320.0727691.3441100
3.93-4.9520.05727931.285199.8
4.95-5020.04827650.985198.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 33.36 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å35.4 Å
Translation2.5 Å35.4 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.1phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→38.29 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.2747 / WRfactor Rwork: 0.2245 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8028 / SU B: 17.476 / SU ML: 0.207 / SU R Cruickshank DPI: 0.4685 / SU Rfree: 0.2649 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.473 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 642 5 %RANDOM
Rwork0.2089 ---
obs0.2109 12901 89.4 %-
all-14430 --
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 max: 70.79 Å2 / Biso mean: 55.054 Å2 / Biso min: 22.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.49 Å2
2---1.38 Å20 Å2
3---1.32 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 0 42 2377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212389
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.9293244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3465298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05423.02196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.86315373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1221512
X-RAY DIFFRACTIONr_chiral_restr0.0980.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021758
X-RAY DIFFRACTIONr_nbd_refined0.2190.2873
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21554
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2120
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.26
X-RAY DIFFRACTIONr_mcbond_it0.731.51546
X-RAY DIFFRACTIONr_mcangle_it1.28422390
X-RAY DIFFRACTIONr_scbond_it1.7633986
X-RAY DIFFRACTIONr_scangle_it2.7234.5853
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 17 -
Rwork0.245 430 -
all-447 -
obs--43.23 %
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)
13.7113-1.6718-0.00816.1554-1.84995.31690.1220.06920.076-0.2405-0.181-0.0007-0.2552-0.04630.0591-0.10.02650.0047-0.2061-0.0126-0.1238-12.88110.497-5.793
23.62931.3581-0.72636.9629-2.15474.57870.0744-0.1143-0.10780.3191-0.1469-0.11360.11450.00750.0725-0.1473-0.0134-0.0034-0.1885-0.023-0.1256-12.025-10.061-32.376
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 217
2X-RAY DIFFRACTION2B1 - 217

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