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- PDB-4p9j: Crystal Structure of rabbit Ryanodine Receptor 1 SPRY2 Domain (10... -

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Basic information

Entry
Database: PDB / ID: 4p9j
TitleCrystal Structure of rabbit Ryanodine Receptor 1 SPRY2 Domain (1070-1246)
ComponentsRyanodine receptor 1
KeywordsTRANSPORT PROTEIN / ion channel / calcium / metal transport / signalling
Function / homology
Function and homology information


ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / cellular response to caffeine / outflow tract morphogenesis / intracellularly gated calcium channel activity ...ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / cellular response to caffeine / outflow tract morphogenesis / intracellularly gated calcium channel activity / organelle membrane / toxic substance binding / smooth endoplasmic reticulum / voltage-gated calcium channel activity / skeletal muscle fiber development / striated muscle contraction / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / cellular response to calcium ion / sarcoplasmic reticulum / muscle contraction / calcium ion transmembrane transport / calcium channel activity / sarcolemma / Z disc / intracellular calcium ion homeostasis / disordered domain specific binding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / calcium ion binding / ATP binding / identical protein binding / membrane
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. / 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 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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 1.1Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Apr 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 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 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
C: Ryanodine receptor 1
A: Ryanodine receptor 1
B: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)60,6623
Polymers60,6623
Non-polymers00
Water7,044391
1
C: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)20,2211
Polymers20,2211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)20,2211
Polymers20,2211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)20,2211
Polymers20,2211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.580, 37.570, 95.820
Angle α, β, γ (deg.)89.97, 89.97, 120.05
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Ryanodine receptor 1 / RyR1 / Skeletal muscle calcium release channel / Skeletal muscle ryanodine receptor / Skeletal ...RyR1 / Skeletal muscle calcium release channel / Skeletal muscle ryanodine receptor / Skeletal muscle-type ryanodine receptor / Type 1 ryanodine receptor


Mass: 20220.623 Da / Num. of mol.: 3 / Fragment: UNP Residues 1070-1246
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RYR1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P11716
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 1.93 Å3/Da / Density % sol: 36.28 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.84→32.55 Å / Num. obs: 36943 / % possible obs: 94 % / Redundancy: 2 % / Net I/σ(I): 8.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1637)refinement
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→32.549 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 22.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2197 1872 5.49 %
Rwork0.1629 --
obs0.1661 34107 86.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.84→32.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4188 0 0 391 4579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134299
X-RAY DIFFRACTIONf_angle_d1.3575837
X-RAY DIFFRACTIONf_dihedral_angle_d14.0751516
X-RAY DIFFRACTIONf_chiral_restr0.054610
X-RAY DIFFRACTIONf_plane_restr0.007778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8401-1.88980.34411110.26932063X-RAY DIFFRACTION73
1.8898-1.94540.31321150.2512159X-RAY DIFFRACTION75
1.9454-2.00820.28961200.23362225X-RAY DIFFRACTION80
2.0082-2.080.27241320.20492453X-RAY DIFFRACTION82
2.08-2.16320.24761440.1922372X-RAY DIFFRACTION85
2.1632-2.26170.27291590.17592496X-RAY DIFFRACTION88
2.2617-2.38090.2451510.172588X-RAY DIFFRACTION89
2.3809-2.530.21991590.17372587X-RAY DIFFRACTION91
2.53-2.72520.25691570.16552644X-RAY DIFFRACTION93
2.7252-2.99930.20321610.16082664X-RAY DIFFRACTION93
2.9993-3.43290.21551580.14372752X-RAY DIFFRACTION94
3.4329-4.32350.13871530.1172630X-RAY DIFFRACTION93
4.3235-32.5540.19161520.13562602X-RAY DIFFRACTION91

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