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- PDB-4esu: Crystal structure of rabbit ryanodine receptor 1 mutant S2776M -

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Basic information

Entry
Database: PDB / ID: 4esu
TitleCrystal structure of rabbit ryanodine receptor 1 mutant S2776M
ComponentsRyanodine receptor 1
KeywordsMETAL TRANSPORT / Ryanodine Receptor Calcium Release Channel / Phosphorylation / Muscle / Skeletal
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
Globin-like - #160 / : / 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 ...Globin-like - #160 / : / 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. / Globin-like / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ryanodine receptor 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsYuchi, Z. / Lau, K. / Van Petegem, F.
CitationJournal: Structure / Year: 2012
Title: Disease mutations in the ryanodine receptor central region: crystal structures of a phosphorylation hot spot domain.
Authors: Yuchi, Z. / Lau, K. / Van Petegem, F.
History
DepositionApr 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Other
Revision 1.2Oct 17, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)25,1666
Polymers24,7061
Non-polymers4605
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.154, 56.193, 113.775
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-3198-

HOH

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Components

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


Mass: 24705.867 Da / Num. of mol.: 1 / Mutation: S2776M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RYR1 / Plasmid: pET28HMT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLacI / References: UniProt: P11716
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.08 Å3/Da / Density % sol: 40.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% PEG3350, 25% Glycerol, 0.1M HEPES, pH 7.0, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2011
Details: Shutterless data collection; Fine phi slicing experiments
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.59→56.89 Å / Num. all: 28427 / Num. obs: 27184 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 26.63 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 12.47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.59-1.640.592.096171183689.2
1.64-1.680.5532.848414198698.6
1.68-1.730.4753.317974191499.1
1.73-1.780.3883.917701190398.5
1.78-1.840.314.636899179598
1.84-1.910.2795.777561176597.8
1.91-1.980.2197.297143166797.1
1.98-2.060.1669.186604158696.1
2.06-2.150.12911.026320159496.6
2.15-2.250.10913.15702146196.6
2.25-2.380.09414.915886140195.9
2.38-2.520.0817.455538133295.6
2.52-2.70.06619.855069125394.3
2.7-2.910.05721.714410113692.5
2.91-3.190.04725.714513107294.9
3.19-3.570.03930.18390896693.2
3.57-4.120.03732.05319283891
4.12-5.040.03134.47303174994.1
5.04-7.130.02932.72234258491.7
7.130.02733.84131334687.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ERT

4ert


Resolution: 1.59→56.89 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.888 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 1361 5 %RANDOM
Rwork0.1963 ---
obs0.198 27144 95.65 %-
all-28427 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.04 Å2 / Biso mean: 22.4985 Å2 / Biso min: 11.53 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å20 Å2-0 Å2
2--1.21 Å2-0 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.59→56.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1498 0 30 144 1672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021645
X-RAY DIFFRACTIONr_angle_refined_deg1.0971.9622240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4185204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24924.70685
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53115290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6081510
X-RAY DIFFRACTIONr_chiral_restr0.0850.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211266
LS refinement shellResolution: 1.594→1.636 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 85 -
Rwork0.303 1586 -
all-1671 -
obs-1836 88.27 %

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