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- PDB-4jkq: Crystal structure of the N-terminal region of the human ryanodine... -

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Basic information

Entry
Database: PDB / ID: 4jkq
TitleCrystal structure of the N-terminal region of the human ryanodine receptor 2
ComponentsRyanodine receptor 2
KeywordsUNKNOWN FUNCTION / beta trefoil fold
Function / homology
Function and homology information


manganese ion transmembrane transport / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / junctional sarcoplasmic reticulum membrane / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis / suramin binding / regulation of AV node cell action potential / sarcoplasmic reticulum calcium ion transport / regulation of SA node cell action potential ...manganese ion transmembrane transport / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / junctional sarcoplasmic reticulum membrane / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis / suramin binding / regulation of AV node cell action potential / sarcoplasmic reticulum calcium ion transport / regulation of SA node cell action potential / calcium ion export / calcium-induced calcium release activity / calcium ion transport into cytosol / embryonic heart tube morphogenesis / cell communication by electrical coupling involved in cardiac conduction / ventricular cardiac muscle cell action potential / cardiac muscle hypertrophy / regulation of ventricular cardiac muscle cell action potential / response to redox state / ryanodine-sensitive calcium-release channel activity / response to caffeine / regulation of cardiac muscle contraction by calcium ion signaling / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to muscle activity / extrinsic component of cytoplasmic side of plasma membrane / cellular response to caffeine / ryanodine receptor complex / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / positive regulation of the force of heart contraction / A band / negative regulation of cytosolic calcium ion concentration / response to muscle stretch / smooth endoplasmic reticulum / intracellularly gated calcium channel activity / response to magnesium ion / detection of calcium ion / regulation of cardiac muscle contraction / regulation of cytosolic calcium ion concentration / positive regulation of heart rate / cardiac muscle contraction / release of sequestered calcium ion into cytosol / Ion homeostasis / regulation of heart rate / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / cellular response to epinephrine stimulus / calcium channel complex / response to nutrient / sarcoplasmic reticulum membrane / calcium-mediated signaling / sarcoplasmic reticulum / striated muscle contraction / sarcolemma / intracellular calcium ion homeostasis / calcium channel activity / Z disc / Stimuli-sensing channels / calcium ion transport / nuclear envelope / scaffold protein binding / response to hypoxia / calmodulin binding / transmembrane transporter binding / response to xenobiotic stimulus / calcium ion binding / enzyme binding / protein-containing complex / membrane / identical protein binding / plasma membrane
Similarity search - Function
IP3 receptor type 1 binding core, RIH 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 ...IP3 receptor type 1 binding core, RIH 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 / Leucine-rich Repeat Variant / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / 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 / Alpha Horseshoe / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Ryanodine receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsBauerova, V. / Sevcik, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural insights into the human RyR2 N-terminal region involved in cardiac arrhythmias.
Authors: Borko, L. / Bauerova-Hlinkova, V. / Hostinova, E. / Gasperik, J. / Beck, K. / Lai, F.A. / Zahradnikova, A. / Sevcik, J.
History
DepositionMar 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: 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: Ryanodine receptor 2


Theoretical massNumber of molelcules
Total (without water)67,9171
Polymers67,9171
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.450, 75.450, 248.840
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 / hRYR-2 / Cardiac muscle ryanodine receptor / Cardiac muscle ryanodine receptor- ...RYR-2 / RyR2 / hRYR-2 / Cardiac muscle ryanodine receptor / Cardiac muscle ryanodine receptor-calcium release channel / Type 2 ryanodine receptor


Mass: 67916.977 Da / Num. of mol.: 1 / Fragment: N-terminal region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RYR2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q92736
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20 mM TRIS-HCl, 150 mM NaCl, 10% glycerol, 7mM mercaptoethanol, 1 mM CHAPS, 0.1% betaine, 100 mM HEPES, 200 mM ammonium formate, 21% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 5, 2012
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.39→124.42 Å / Num. obs: 29469 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 13.8 % / Rmerge(I) obs: 0.16 / Rsym value: 0.15 / Net I/σ(I): 12.2
Reflection shellResolution: 2.39→2.52 Å / % possible all: 95

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2XOA

2xoa


Resolution: 2.39→44.77 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.912 / SU B: 18.374 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.316 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26087 1444 4.9 %RANDOM
Rwork0.22405 ---
obs0.2258 27960 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.542 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å2-0 Å20 Å2
2--1.84 Å20 Å2
3----3.68 Å2
Refinement stepCycle: LAST / Resolution: 2.39→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3934 0 0 79 4013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194009
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.9465411
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9085496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94123.316190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95915708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9431533
X-RAY DIFFRACTIONr_chiral_restr0.0820.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023010
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.88633986
X-RAY DIFFRACTIONr_sphericity_free74.934534
X-RAY DIFFRACTIONr_sphericity_bonded26.95653927
LS refinement shellResolution: 2.39→2.449 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 74 -
Rwork0.336 1598 -
obs--90.04 %
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)
11.910.18960.05351.01970.11224.35550.0572-0.0460.0118-0.02850.00620.0254-0.1208-0.0735-0.06340.23560.06850.0560.135-0.06660.130520.411-32.984-49.423
23.1634-0.7673-1.09582.8850.47185.4209-0.2331-0.43060.13340.30510.2637-0.1270.13890.6109-0.03060.40380.2465-0.02980.2238-0.02820.009422.385-25.446-17.451
30.88071.168-0.72612.3923-1.34952.96270.0821-0.06090.1038-0.0320.0160.20.19270.3262-0.09810.20790.10320.01360.13050.00580.14278.131-7.224-38.918
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 223
2X-RAY DIFFRACTION2A224 - 408
3X-RAY DIFFRACTION3A409 - 544

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