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- PDB-6j6p: Crystal structure of diamondback moth ryanodine receptor phosphor... -

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Basic information

Entry
Database: PDB / ID: 6j6p
TitleCrystal structure of diamondback moth ryanodine receptor phosphorylation domain(2836-3050) mutant S2946D
ComponentsRyanodine receptor
KeywordsMETAL TRANSPORT / diamondback moth / ryanodine receptor / phosphorylation domain / TRANSPORT PROTEIN
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 / calcium channel complex / sarcoplasmic reticulum membrane / sarcolemma / Z disc / intracellular calcium ion homeostasis
Similarity search - Function
Globin-like - #160 / : / 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 ...Globin-like - #160 / : / 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 / 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
Biological speciesPlutella xylostella (diamondback moth)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsXu, T. / Lin, L. / Yuchi, Z.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China) China
CitationJournal: Bmc Biol. / Year: 2019
Title: Crystal structure of diamondback moth ryanodine receptor Repeat34 domain reveals insect-specific phosphorylation sites.
Authors: Xu, T. / Yuchi, Z.
History
DepositionJan 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.3Nov 22, 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
A: Ryanodine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,27912
Polymers25,2331
Non-polymers1,04611
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-8 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.828, 55.828, 131.552
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Ryanodine receptor


Mass: 25233.080 Da / Num. of mol.: 1 / Fragment: phosphorylation domain / Mutation: S2946D, D3023A, K3024A, K3027A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plutella xylostella (diamondback moth) / Gene: RyR / Production host: Escherichia coli (E. coli) / References: UniProt: I3NWV8
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2% v/v PEG 400, 0.1M Sodium HEPES pH 7.5, 2.0M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 36640 / % possible obs: 99.6 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.038 / Rrim(I) all: 0.116 / Χ2: 0.722 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.53-1.564.60.50717340.80.2570.5710.49694.1
1.56-1.585.50.5217660.8350.2390.5750.52298.6
1.58-1.626.50.54617840.8740.230.5940.653100
1.62-1.6570.51218320.90.2060.5530.771100
1.65-1.687.30.51617840.8960.2030.5550.874100
1.68-1.727.50.54518250.9090.2110.5860.958100
1.72-1.777.60.55518010.90.2130.5961.09100
1.77-1.817.50.49918210.9420.1930.5361.089100
1.81-1.878.10.47618350.9510.1760.5091.045100
1.87-1.938.80.45117900.9670.160.4790.958100
1.93-29.20.38618470.9830.1330.4090.802100
2-2.089.30.30817990.9890.1050.3260.584100
2.08-2.1790.24918340.9910.0870.2640.5799.9
2.17-2.299.60.2218240.9950.0740.2320.578100
2.29-2.43100.17718690.9960.0580.1870.569100
2.43-2.629.80.14418290.9970.0480.1520.558100
2.62-2.889.20.10518580.9970.0370.1120.565100
2.88-3.310.10.08118860.9980.0270.0850.602100
3.3-4.159.30.05818840.9990.020.0610.671100
4.15-5090.04920380.9990.0170.0520.61199.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3247refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ETV, 5C30

4etv

5c30


Resolution: 1.53→32.481 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.66
RfactorNum. reflection% reflection
Rfree0.2254 2007 5.49 %
Rwork0.1906 --
obs0.1925 36583 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.94 Å2 / Biso mean: 26.7647 Å2 / Biso min: 11.99 Å2
Refinement stepCycle: final / Resolution: 1.53→32.481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 65 214 1825
Biso mean--49 36.12 -
Num. residues----192
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5302-1.56850.24421370.24152322245995
1.5685-1.61090.27141380.229224402578100
1.6109-1.65830.261420.231824272569100
1.6583-1.71180.28791430.252524222565100
1.7118-1.7730.2691440.24524442588100
1.773-1.8440.23351440.221624512595100
1.844-1.92790.22711430.210124632606100
1.9279-2.02950.2631450.208724442589100
2.0295-2.15660.2441420.19624772619100
2.1566-2.32310.23171440.184624852629100
2.3231-2.55680.21041380.187424922630100
2.5568-2.92660.22811470.185725152662100
2.9266-3.68630.22041450.173625312676100
3.6863-32.48840.19711550.172826632818100

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