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- PDB-4p9i: Crystal Structure of mouse Ryanodine Receptor 2 SPRY2 Domain (108... -

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Basic information

Entry
Database: PDB / ID: 4p9i
TitleCrystal Structure of mouse Ryanodine Receptor 2 SPRY2 Domain (1080-1253)
ComponentsRyanodine receptor 2
KeywordsTRANSPORT PROTEIN / ion channel / signalling / metal transport
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 / response to muscle activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / calcium ion transport into cytosol / regulation of cardiac muscle contraction by calcium ion signaling / 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 / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / striated muscle contraction / release of sequestered calcium ion into cytosol / cardiac muscle contraction / extrinsic component of cytoplasmic side of plasma membrane / monoatomic ion transmembrane transport / sarcoplasmic reticulum membrane / cellular response to epinephrine stimulus / calcium channel complex / 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 / response to calcium ion / intracellular calcium ion homeostasis / calcium ion transport / : / nuclear envelope / scaffold protein binding / calmodulin binding / response to hypoxia / calcium ion binding / protein kinase binding / enzyme binding / protein-containing complex / membrane / identical protein binding
Similarity search - Function
SPRY 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 ...SPRY 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. / 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
Ryanodine receptor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3401 Å
AuthorsLau, K. / Van Petegem, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nat Commun / Year: 2014
Title: Crystal structures of wild type and disease mutant forms of the ryanodine receptor SPRY2 domain.
Authors: Lau, K. / Van Petegem, F.
History
DepositionApr 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
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)19,6221
Polymers19,6221
Non-polymers00
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8400 Å2
2
A: Ryanodine receptor 2

A: Ryanodine receptor 2


Theoretical massNumber of molelcules
Total (without water)39,2442
Polymers39,2442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area2150 Å2
ΔGint-12 kcal/mol
Surface area14650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.290, 66.230, 66.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-1338-

HOH

21A-1413-

HOH

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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: 19621.994 Da / Num. of mol.: 1 / Fragment: UNP residues 1080-1253
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.17 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: sodium formate, peg 3350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.34→47.095 Å / Num. obs: 33935 / % possible obs: 91.6 % / Redundancy: 6 % / Net I/σ(I): 17.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1637)refinement
XDSdata scaling
XDSdata reduction
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3401→47.095 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / Phase error: 15.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1631 1697 5 %
Rwork0.1376 --
obs0.1389 33932 91.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3401→47.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1288 0 0 227 1515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071325
X-RAY DIFFRACTIONf_angle_d1.1681787
X-RAY DIFFRACTIONf_dihedral_angle_d11.352463
X-RAY DIFFRACTIONf_chiral_restr0.073179
X-RAY DIFFRACTIONf_plane_restr0.005234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3401-1.37950.2065820.14771571X-RAY DIFFRACTION55
1.3795-1.4240.17341050.13591981X-RAY DIFFRACTION68
1.424-1.47490.14891250.12572376X-RAY DIFFRACTION83
1.4749-1.5340.21691430.12272720X-RAY DIFFRACTION94
1.534-1.60380.15831530.1122901X-RAY DIFFRACTION100
1.6038-1.68840.15471520.10922898X-RAY DIFFRACTION100
1.6884-1.79410.15581530.11832908X-RAY DIFFRACTION100
1.7941-1.93270.16381540.12432906X-RAY DIFFRACTION100
1.9327-2.12720.14431540.12362930X-RAY DIFFRACTION100
2.1272-2.43490.15781550.13122940X-RAY DIFFRACTION99
2.4349-3.06770.16361570.15262985X-RAY DIFFRACTION100
3.0677-47.12370.16721640.15523119X-RAY DIFFRACTION100

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