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- PDB-6lt9: The crystal structure of diamondback moth ryanodine receptor SPRY... -

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Basic information

Entry
Database: PDB / ID: 6lt9
TitleThe crystal structure of diamondback moth ryanodine receptor SPRY1 domain
ComponentsRyanodine receptor 1
KeywordsMEMBRANE PROTEIN / diamondback moth / ryanodine receptor / SPRY1
Function / homology
Function and homology information


ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / smooth endoplasmic reticulum / striated muscle contraction / sarcoplasmic reticulum membrane / calcium channel complex / sarcolemma / Z disc / intracellular calcium ion homeostasis
Similarity search - Function
SPRY 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 ...SPRY 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/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 / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ryanodine receptor 1
Similarity search - Component
Biological speciesPlutella xylostella (diamondback moth)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsZhou, Y. / Lin, L. / Yuchi, Z.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFD0201400 China
Ministry of Science and Technology (MoST, China)2017YFD0201403 China
CitationJournal: To Be Published
Title: The crystal structure of diamondback moth ryanodine receptor SPRY1 domain
Authors: Nayak, B. / Zhou, Y. / Salauddin, N. / Lin, L. / You, M. / You, S. / Yuchi, Z.
History
DepositionJan 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: Ryanodine receptor 1
B: Ryanodine receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5178
Polymers43,1032
Non-polymers4146
Water4,252236
1
F: Ryanodine receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6673
Polymers21,5521
Non-polymers1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-9 kcal/mol
Surface area9210 Å2
MethodPISA
2
B: Ryanodine receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8515
Polymers21,5521
Non-polymers2994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-9 kcal/mol
Surface area8960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.893, 64.893, 95.767
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Ryanodine receptor 1


Mass: 21551.535 Da / Num. of mol.: 2 / Mutation: R735A, E817P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plutella xylostella (diamondback moth) / Production host: Escherichia coli (E. coli) / References: UniProt: G8EME3
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 2M Ammonium, 0.2M sodium chloride, 0.1M sodium cacodylate, ph 6.5.

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Data collection

DiffractionMean temperature: 193.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Jun 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 36452 / % possible obs: 99.3 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.044 / Rrim(I) all: 0.112 / Χ2: 0.482 / Net I/σ(I): 4.7 / Num. measured all: 212691
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.832.30.36516550.7260.2770.4620.43590.6
1.83-1.862.70.37217590.7630.2660.4610.43496.6
1.86-1.93.10.38218190.7890.2550.4620.45398.8
1.9-1.943.80.33817900.8710.20.3950.45499.9
1.94-1.984.60.33318410.9060.1740.3770.45899.9
1.98-2.035.90.30918330.9680.1380.3390.462100
2.03-2.086.40.29218260.9750.1250.3180.465100
2.08-2.136.60.25118230.9830.1060.2720.477100
2.13-2.26.60.24718350.9830.1040.2690.472100
2.2-2.276.50.2218360.9870.0940.2390.485100
2.27-2.356.30.20318270.9870.0880.2220.474100
2.35-2.446.90.19718260.9910.080.2130.473100
2.44-2.5570.17818540.9920.0720.1920.476100
2.55-2.696.80.15618390.9930.0640.1690.46100
2.69-2.866.40.12918090.9940.0550.140.487100
2.86-3.0870.10118520.9960.0410.1090.479100
3.08-3.3970.07718520.9970.0310.0830.508100
3.39-3.886.60.05918310.9980.0250.0640.496100
3.88-4.887.10.04918480.9980.020.0530.522100
4.88-506.50.05218970.9980.0220.0570.555100

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Processing

Software
NameVersionClassification
PHENIX1.14_3247refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C33

5c33


Resolution: 1.801→23.942 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.62
RfactorNum. reflection% reflection
Rfree0.2165 1824 5.64 %
Rwork0.1865 --
obs0.1883 32332 88.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 48.31 Å2 / Biso mean: 18.6917 Å2 / Biso min: 7.28 Å2
Refinement stepCycle: final / Resolution: 1.801→23.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2724 0 58 236 3018
Biso mean--25.34 24.62 -
Num. residues----362
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.801-1.84920.28231120.2206194173
1.8492-1.90360.25851280.211211880
1.9036-1.9650.21441320.1919229586
1.965-2.03520.24951380.1808231287
2.0352-2.11660.19141330.1756233488
2.1166-2.21290.22991420.1795237189
2.2129-2.32950.23761430.1898237289
2.3295-2.47530.26191450.1964238289
2.4753-2.66620.22361510.2007236890
2.6662-2.9340.22831460.1964249193
2.934-3.35760.20751520.1811249794
3.3576-4.22640.19821490.1708257296
4.2264-23.9420.18581530.1851245591

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