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- PDB-5c30: Crystal Structure of Rabbit Ryanodine Receptor 1 Repeat12 Domain -

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Basic information

Entry
Database: PDB / ID: 5c30
TitleCrystal Structure of Rabbit Ryanodine Receptor 1 Repeat12 Domain
ComponentsRyanodine receptor 1
KeywordsCONTRACTILE PROTEIN / Repeat motif
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 / intracellularly gated calcium channel activity / outflow tract morphogenesis ...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 / intracellularly gated calcium channel activity / outflow tract morphogenesis / organelle membrane / toxic substance binding / voltage-gated calcium channel activity / skeletal muscle fiber development / 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 / intracellular calcium ion homeostasis / disordered domain specific binding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / calcium ion binding / ATP binding / membrane / identical protein binding
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. / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Ryanodine receptor 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsYuchi, Z. / Van Petegem, F.
Funding support Canada, United States, 3items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-119608 Canada
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R01AR059124 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL092097 United States
CitationJournal: Nat Commun / Year: 2015
Title: Crystal structures of ryanodine receptor SPRY1 and tandem-repeat domains reveal a critical FKBP12 binding determinant.
Authors: Yuchi, Z. / Yuen, S.M. / Lau, K. / Underhill, A.Q. / Cornea, R.L. / Fessenden, J.D. / Van Petegem, F.
History
DepositionJun 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9762
Polymers22,9161
Non-polymers601
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint2 kcal/mol
Surface area10740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.440, 94.440, 67.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1565-

HOH

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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: 22916.008 Da / Num. of mol.: 1 / Fragment: repeat12 domain (UNP residues 857-1054) / Mutation: C906A, C937A, C1040A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RYR1 / Plasmid: pET28-HMT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta(DE3) / References: UniProt: P11716
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.82 Å3/Da / Density % sol: 67.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES, pH 7.0, 19% w/v PEG20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 2, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.55→47.22 Å / Num. obs: 50032 / % possible obs: 99.2 % / Redundancy: 11.9 % / Biso Wilson estimate: 19.82 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 13.82
Reflection shellResolution: 1.55→1.605 Å / Redundancy: 12.1 % / Rmerge(I) obs: 1.509 / Mean I/σ(I) obs: 2.17 / % possible all: 98.14

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→47.22 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 16.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1645 1869 3.74 %
Rwork0.1491 --
obs0.1497 50026 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→47.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1500 0 4 388 1892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111672
X-RAY DIFFRACTIONf_angle_d1.3552288
X-RAY DIFFRACTIONf_dihedral_angle_d12.25644
X-RAY DIFFRACTIONf_chiral_restr0.059245
X-RAY DIFFRACTIONf_plane_restr0.008307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.5920.27131430.23893653X-RAY DIFFRACTION98
1.592-1.63880.25751380.20873610X-RAY DIFFRACTION98
1.6388-1.69170.20521390.18863641X-RAY DIFFRACTION99
1.6917-1.75220.20961440.18443676X-RAY DIFFRACTION99
1.7522-1.82230.18471410.16683641X-RAY DIFFRACTION98
1.8223-1.90530.20291450.15813680X-RAY DIFFRACTION99
1.9053-2.00570.14961440.15373688X-RAY DIFFRACTION99
2.0057-2.13140.16641420.14383673X-RAY DIFFRACTION99
2.1314-2.29590.15261410.13613718X-RAY DIFFRACTION99
2.2959-2.5270.14161430.13493736X-RAY DIFFRACTION100
2.527-2.89260.14421480.13793750X-RAY DIFFRACTION100
2.8926-3.64420.16671510.1343789X-RAY DIFFRACTION100
3.6442-47.24190.15371500.15143902X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.1552 Å / Origin y: 73.8508 Å / Origin z: 70.6741 Å
111213212223313233
T0.1476 Å20.0127 Å2-0.0014 Å2-0.0998 Å20.0088 Å2--0.1538 Å2
L0.7958 °20.4128 °20.0026 °2-1.538 °20.4466 °2--2.0877 °2
S-0.0148 Å °-0.0044 Å °0.0612 Å °-0.0717 Å °-0.0005 Å °0.0755 Å °-0.1205 Å °-0.0425 Å °0.0108 Å °
Refinement TLS groupSelection details: all

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