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- PDB-4i0y: CRYSTAL STRUCTURE OF RABBIT RYANODINE RECEPTOR 1 (RESIDUES 1-536)... -

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Basic information

Entry
Database: PDB / ID: 4i0y
TitleCRYSTAL STRUCTURE OF RABBIT RYANODINE RECEPTOR 1 (RESIDUES 1-536) DISEASE MUTANT C36R
ComponentsRyanodine receptor 1
KeywordsMETAL TRANSPORT / calcium channel / ER/SR membrane
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 / organelle membrane / cellular response to caffeine / 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 / organelle membrane / cellular response to caffeine / outflow tract morphogenesis / intracellularly gated calcium channel activity / toxic substance binding / voltage-gated calcium channel activity / smooth endoplasmic reticulum / skeletal muscle fiber development / striated muscle contraction / release of sequestered calcium ion into cytosol / muscle contraction / sarcoplasmic reticulum membrane / cellular response to calcium ion / sarcoplasmic reticulum / 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
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 / 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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / 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 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVan Petegem, F. / Kimlicka, L.
CitationJournal: Nat Commun / Year: 2013
Title: Disease mutations in the ryanodine receptor N-terminal region couple to a mobile intersubunit interface.
Authors: Kimlicka, L. / Lau, K. / Tung, C.C. / Van Petegem, F.
History
DepositionNov 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)59,6232
Polymers59,5301
Non-polymers921
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)170.381, 170.381, 302.113
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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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: 59530.430 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DISEASE HOT SPOT, RESIDUES 1-536 / Mutation: C36R
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 7.09 Å3/Da / Density % sol: 82.65 %
Crystal growMethod: evaporation / pH: 9.5 / Details: pH 9.5, EVAPORATION

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 23, 2010
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.8→49.18 Å / Num. all: 476570 / Num. obs: 41758 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.4 % / Net I/σ(I): 18
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible all
2.8-2.9511.51100
2.95-3.1311.51100
3.13-3.3511.51100
3.35-3.6111.51100
3.61-3.9611.51100
3.96-4.4311.41100

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
REFMAC5refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→49.18 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.92 / SU B: 20.835 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2465 2088 5 %RANDOM
Rwork0.2426 ---
all0.2426 41758 --
obs0.24284 39670 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.976 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å2-0.99 Å20 Å2
2---1.98 Å20 Å2
3---2.97 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 6 17 3518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213566
X-RAY DIFFRACTIONr_angle_refined_deg0.9751.9534849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9995464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47322.929140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.12815521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2651523
X-RAY DIFFRACTIONr_chiral_restr0.060.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212672
X-RAY DIFFRACTIONr_mcbond_it0.2411.52339
X-RAY DIFFRACTIONr_mcangle_it0.45623674
X-RAY DIFFRACTIONr_scbond_it0.44331227
X-RAY DIFFRACTIONr_scangle_it0.7724.51175
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 152 -
Rwork0.332 2909 -
obs--100 %
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)
16.38330.93950.47723.41580.29416.38310.2965-0.2843-0.33730.32180.0494-0.21250.01790.1841-0.34580.638-0.1335-0.19960.9753-0.10930.2719-45.97853.797-9.671
23.92670.1522-0.30671.5885-0.33061.80.1617-0.0830.33360.13260.078-0.184-0.24430.0729-0.23970.578-0.05020.03230.5643-0.090.1011-71.47862.15-25.063
34.2056-0.2946-1.59212.4319-0.08385.69230.16720.1768-0.12920.03940.1225-0.4376-0.23150.858-0.28960.4335-0.0863-0.02620.9247-0.21250.1694-45.98354.536-40.598
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 205
2X-RAY DIFFRACTION2A206 - 394
3X-RAY DIFFRACTION3A395 - 532

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