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- PDB-4erv: Crystal structure of human ryanodine receptor 3 (2597-2800) -

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Basic information

Entry
Database: PDB / ID: 4erv
TitleCrystal structure of human ryanodine receptor 3 (2597-2800)
ComponentsRyanodine receptor 3
KeywordsMETAL TRANSPORT / Ryanodine Receptor Calcium Release Channel
Function / homology
Function and homology information


calcium-induced calcium release activity / cellular response to magnesium ion / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cellular response to ATP / cellular response to caffeine / intracellularly gated calcium channel activity / smooth endoplasmic reticulum / striated muscle contraction / release of sequestered calcium ion into cytosol ...calcium-induced calcium release activity / cellular response to magnesium ion / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cellular response to ATP / cellular response to caffeine / intracellularly gated calcium channel activity / smooth endoplasmic reticulum / striated muscle contraction / release of sequestered calcium ion into cytosol / Ion homeostasis / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to calcium ion / calcium ion transmembrane transport / Stimuli-sensing channels / sarcolemma / Z disc / intracellular calcium ion homeostasis / calcium ion transport / protein homotetramerization / calmodulin binding / calcium ion 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 / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ryanodine receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 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 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3067
Polymers23,7421
Non-polymers5646
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ryanodine receptor 3
hetero molecules

A: Ryanodine receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,61314
Polymers47,4842
Non-polymers1,12912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area5970 Å2
ΔGint-111 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.570, 58.540, 47.460
Angle α, β, γ (deg.)90.000, 97.210, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ryanodine receptor 3 / RYR-3 / RyR3 / Brain ryanodine receptor-calcium release channel / Brain-type ryanodine receptor / ...RYR-3 / RyR3 / Brain ryanodine receptor-calcium release channel / Brain-type ryanodine receptor / Type 3 ryanodine receptor


Mass: 23741.969 Da / Num. of mol.: 1 / Mutation: K2775A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RYR3, HBRR / Plasmid: pET28HMT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLacI / References: UniProt: Q15413
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 1.4M Ammonium sulfate, 0.1M Bicine, pH 9.5, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 29, 2011 / Details: Double Crystal Monochromator, mirrors
RadiationMonochromator: Double Crystal Monochromator with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 25284 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 34.27 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 20.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.75-1.80.4523.156841187199.2
1.8-1.840.343.926711182699.1
1.84-1.90.2695.126382174996.6
1.9-1.960.2136.525836166094.9
1.96-2.020.1438.886200168199
2.02-2.090.10612.195486157597.4
2.09-2.170.08114.495751156598.7
2.17-2.260.06717.355204148396.5
2.26-2.360.05320.575118140697.1
2.36-2.470.04723.045103137698.6
2.47-2.610.04325.374928132098.5
2.61-2.770.0428.854536125098.4
2.77-2.960.03531.814315116299.1
2.96-3.20.02737.84080109499
3.2-3.50.02541.213715101499.1
3.5-3.910.02443.62329691198.6
3.91-4.520.02445.89299181098.5
4.52-5.530.02146.71254768498.8
5.53-7.830.02345.03198454699.5
7.830.02747.13105030197.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
MxDCGUIdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→35.35 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 1265 5 %RANDOM
Rwork0.1899 ---
obs0.1914 25283 98.09 %-
all-25284 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 59.04 Å2 / Biso mean: 26.9336 Å2 / Biso min: 16.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å2-0.7 Å2
2---1.44 Å2-0 Å2
3---1.89 Å2
Refinement stepCycle: LAST / Resolution: 1.75→35.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1528 0 33 209 1770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021600
X-RAY DIFFRACTIONr_angle_refined_deg1.2141.9792167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1445195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29724.39466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90215275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.178157
X-RAY DIFFRACTIONr_chiral_restr0.0750.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211169
X-RAY DIFFRACTIONr_rigid_bond_restr4.24531600
X-RAY DIFFRACTIONr_sphericity_free05209
X-RAY DIFFRACTIONr_sphericity_bonded051569
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 94 -
Rwork0.226 1776 -
all-1870 -
obs-1871 99.1 %

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