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- PDB-4etv: Crystal structure of mouse ryanodine receptor 2 (2699-2904) -

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Basic information

Entry
Database: PDB / ID: 4etv
TitleCrystal structure of mouse ryanodine receptor 2 (2699-2904)
ComponentsRyanodine receptor 2
KeywordsMETAL TRANSPORT / Ryanodine Receptor Calcium Release Channel / Phosphorylation / Muscle / Cardiac
Function / homology
Function and homology information


establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / regulation of atrial cardiac muscle cell action potential / suramin binding / left ventricular cardiac muscle tissue morphogenesis / regulation of AV node cell action potential / regulation of SA node cell action potential / : / Stimuli-sensing channels ...establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / regulation of atrial cardiac muscle cell action potential / suramin binding / left ventricular cardiac muscle tissue morphogenesis / regulation of AV node cell action potential / regulation of SA node cell action potential / : / Stimuli-sensing channels / regulation of ventricular cardiac muscle cell action potential / ventricular cardiac muscle cell action potential / Ion homeostasis / positive regulation of sequestering of calcium ion / embryonic heart tube morphogenesis / cardiac muscle hypertrophy / calcium ion transport into cytosol / ryanodine-sensitive calcium-release channel activity / response to caffeine / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to redox state / calcium ion transmembrane import into cytosol / response to muscle activity / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / cellular response to caffeine / positive regulation of the force of heart contraction / intracellularly gated calcium channel activity / detection of calcium ion / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / smooth endoplasmic reticulum / positive regulation of heart rate / response to muscle stretch / sarcoplasmic reticulum membrane / cellular response to epinephrine stimulus / calcium channel complex / regulation of heart rate / sarcomere / sarcoplasmic reticulum / establishment of localization in cell / calcium-mediated signaling / calcium ion transmembrane transport / calcium channel activity / Z disc / intracellular calcium ion homeostasis / calcium ion transport / response to hypoxia / calmodulin binding / calcium ion binding / protein kinase binding / enzyme binding / protein-containing complex / identical protein binding / membrane
Similarity search - Function
Globin-like - #160 / 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 ...Globin-like - #160 / 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 / 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 / Globin-like / EF-hand domain pair / EF-hand domain / 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 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 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 24, 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 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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 2
B: Ryanodine receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3013
Polymers49,2662
Non-polymers351
Water5,927329
1
A: Ryanodine receptor 2


Theoretical massNumber of molelcules
Total (without water)24,6331
Polymers24,6331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ryanodine receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6682
Polymers24,6331
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-13 kcal/mol
Surface area18470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.900, 88.220, 92.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ryanodine receptor 2 / RYR-2 / RyR2 / Cardiac muscle ryanodine receptor / Cardiac muscle ryanodine receptor-calcium ...RYR-2 / RyR2 / Cardiac muscle ryanodine receptor / Cardiac muscle ryanodine receptor-calcium release channel / Type 2 ryanodine receptor


Mass: 24632.764 Da / Num. of mol.: 2 / Mutation: K2879A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ryr2 / Plasmid: pET28HMT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLacI / References: UniProt: E9Q401
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Mutation: K2879A / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 9% PEG3350, 0.1M Bicine, pH 9, 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: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 58433 / Num. obs: 58410 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.434 Å2 / Rmerge(I) obs: 0.141 / Net I/σ(I): 9.69
Reflection shell

Rmerge(I) obs: 0.016 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.65-1.691.94307364241100
1.69-1.742.37305454192100
1.74-1.792.9297664043100
1.79-1.843.55291323953100
1.84-1.914.4630107377399.9
1.91-1.976.91546983711100
1.97-2.059.26526193572100
2.05-2.1311.26501773430100
2.13-2.2212.87481343304100
2.22-2.3314.45457213178100
2.33-2.4615.84430273014100
2.46-2.6117.24403432841100
2.61-2.7915.34287672703100
2.79-3.0113.07166602514100
3.01-3.314.2215212232999.9
3.3-3.6914.96136572129100
3.69-4.2615.4911870186699.9
4.26-5.2215.510003160599.9
5.22-7.3814.787533127899.8
7.3814.92405673499.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
MxDCGUIdata collection
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→49.05 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / 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
Rfree0.2501 2921 5 %RANDOM
Rwork0.2282 ---
obs0.2293 55490 99.92 %-
all-58433 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.38 Å2 / Biso mean: 29.3668 Å2 / Biso min: 9.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å2-0 Å20 Å2
2---0.79 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.65→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2628 0 1 329 2958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022738
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.9613710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6295332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.77924.524126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72715448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1871511
X-RAY DIFFRACTIONr_chiral_restr0.090.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212063
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 212 -
Rwork0.286 4022 -
all-4234 -
obs-4241 99.86 %

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