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- PDB-3ila: Crystal structure of rabbit ryanodine receptor 1 N-terminal domai... -

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Entry
Database: PDB / ID: 3ila
TitleCrystal structure of rabbit ryanodine receptor 1 N-terminal domain (9-205)
ComponentsRyanodine receptor 1
KeywordsSIGNALING PROTEIN / BETA TREFOIL / Calcium channel / Calcium transport / Glycoprotein / Ion transport / Ionic channel / Membrane / Phosphoprotein / Receptor / S-nitrosylation / Transmembrane / Transport
Function / homology
Function and homology information


ATP-gated ion channel activity / terminal cisterna / ryanodine-sensitive calcium-release channel activity / ryanodine receptor complex / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / cellular response to caffeine / skin development / organelle membrane / intracellularly gated calcium channel activity ...ATP-gated ion channel activity / terminal cisterna / ryanodine-sensitive calcium-release channel activity / ryanodine receptor complex / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / cellular response to caffeine / skin development / organelle membrane / intracellularly gated calcium channel activity / smooth endoplasmic reticulum / outflow tract morphogenesis / toxic substance binding / striated muscle contraction / voltage-gated calcium channel activity / skeletal muscle fiber development / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / muscle contraction / cellular response to calcium ion / sarcoplasmic reticulum / sarcolemma / calcium ion transmembrane transport / calcium channel activity / 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
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 ...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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / 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 / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
Ryanodine receptor 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLobo, P.A. / Van Petegem, F.
CitationJournal: Structure / Year: 2009
Title: Crystal structures of the N-terminal domains of cardiac and skeletal muscle ryanodine receptors: insights into disease mutations.
Authors: Lobo, P.A. / Van Petegem, F.
History
DepositionAug 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ryanodine receptor 1
B: Ryanodine receptor 1
C: Ryanodine receptor 1
D: Ryanodine receptor 1
E: Ryanodine receptor 1
F: Ryanodine receptor 1
G: Ryanodine receptor 1
H: Ryanodine receptor 1
I: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)195,9459
Polymers195,9459
Non-polymers00
Water00
1
A: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)21,7721
Polymers21,7721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)21,7721
Polymers21,7721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)21,7721
Polymers21,7721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)21,7721
Polymers21,7721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)21,7721
Polymers21,7721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)21,7721
Polymers21,7721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)21,7721
Polymers21,7721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)21,7721
Polymers21,7721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)21,7721
Polymers21,7721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.734, 155.705, 81.613
Angle α, β, γ (deg.)90.00, 110.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 21771.654 Da / Num. of mol.: 9 / Fragment: N-Terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RYR1 / Plasmid: pET28 HMT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 placI / References: UniProt: P11716

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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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15-25% PEG 3350, 0.2M sodium chloride, 0.1M BisTris, pH 7.0, 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: 0.97949 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 27, 2008 / 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: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 36063 / Num. obs: 32354 / % possible obs: 69.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 59.146 Å2 / Rsym value: 0.14 / Net I/σ(I): 13.28
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.33 / Num. unique all: 1837 / Rsym value: 0.416 / % possible all: 45.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ryanodine Receptor isoform 2

Resolution: 2.9→48.51 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.823 / SU B: 52.997 / SU ML: 0.481 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.536 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31991 1736 5.1 %RANDOM
Rwork0.27413 ---
all0.27653 34226 --
obs0.27653 28582 93.12 %-
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 mean: 67.983 Å2
Baniso -1Baniso -2Baniso -3
1-6.53 Å20 Å2-0.08 Å2
2---3.67 Å20 Å2
3----2.91 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9944 0 0 0 9944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02110079
X-RAY DIFFRACTIONr_angle_refined_deg0.7841.9613697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.98251326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.31723.894339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.061151393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0111534
X-RAY DIFFRACTIONr_chiral_restr0.0460.21710
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.027291
X-RAY DIFFRACTIONr_nbd_refined0.1320.23344
X-RAY DIFFRACTIONr_nbtor_refined0.2780.26571
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2286
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0950.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.25
X-RAY DIFFRACTIONr_mcbond_it0.1241.57056
X-RAY DIFFRACTIONr_mcangle_it0.225210665
X-RAY DIFFRACTIONr_scbond_it0.16533505
X-RAY DIFFRACTIONr_scangle_it0.2634.53032
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 89 -
Rwork0.293 1710 -
obs--67.4 %
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)
12.0740.1118-1.00043.545-1.06894.4058-0.0170.04560.12710.1542-0.0460.1891-0.2102-0.0220.063-0.40230.0166-0.0385-0.2792-0.0339-0.2861-11.00248.363623.4148
23.25170.3623-0.90962.7835-1.44054.2586-0.08860.0726-0.2250.01070.1095-0.1705-0.34320.1833-0.0209-0.3917-0.06190.019-0.26-0.061-0.307220.43955.74581.7602
32.05680.70930.31554.66682.07485.4032-0.0149-0.0380.00450.0824-0.10160.22880.2251-0.27720.1165-0.4326-0.0478-0.0397-0.27270.0184-0.353-19.1337-16.61211.407
42.225-0.82830.3716.9187-1.94083.8966-0.03510.0114-0.0994-0.0429-0.09-0.0519-0.0865-0.0050.1251-0.3244-0.02170.0617-0.38420.0025-0.3554-19.8068-42.600425.0199
51.62880.020.46533.43390.9723.73490.0813-0.0213-0.00130.1307-0.087-0.05760.18560.05770.0057-0.3325-0.06920.0076-0.28630.0439-0.366-13.1427-20.304149.6144
61.58950.5098-0.334.6959-1.0163.39450.0603-0.01730.0717-0.0361-0.06770.1128-0.0986-0.11580.0074-0.37590.00560.0009-0.32140.0149-0.351122.229310.469249.8009
71.7090.6666-0.33475.35730.12463.63440.0718-0.0550.12320.1608-0.07110.02020.432-0.1651-0.0007-0.2940.0009-0.0549-0.3461-0.0026-0.41217.5126-45.079352.2736
82.8066-0.80761.01693.5887-0.89743.47820.056-0.0508-0.17430.0230.27240.40050.00090.0047-0.3284-0.43840.05030.0417-0.32410.1185-0.221416.5457-18.690324.5892
93.32430.55160.11373.9852-1.96793.6209-0.0639-0.06510.5505-1.0366-0.14920.31230.39470.39230.2131-0.49020.0744-0.0376-0.41360.0649-0.280519.2363-44.19046.5785
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 205
2X-RAY DIFFRACTION2B1 - 205
3X-RAY DIFFRACTION3C1 - 205
4X-RAY DIFFRACTION4D1 - 205
5X-RAY DIFFRACTION5E1 - 205
6X-RAY DIFFRACTION6F1 - 205
7X-RAY DIFFRACTION7G1 - 205
8X-RAY DIFFRACTION8H1 - 205
9X-RAY DIFFRACTION9I1 - 205

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