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- PDB-6lqk: Crystal structure of honeybee RyR NTD -

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Basic information

Entry
Database: PDB / ID: 6lqk
TitleCrystal structure of honeybee RyR NTD
Componentsryanodine receptor
KeywordsMEMBRANE PROTEIN / honey bee / ryanodine receptor / n-terminal domain / crystal structure.
Function / homology
Function and homology information


ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / membrane => GO:0016020
Similarity search - Function
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 ...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. / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.499 Å
AuthorsZhou, Y. / Lin, L. / Yuchi, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31972287 China
National Natural Science Foundation of China (NSFC)31972271 China
CitationJournal: Insect Biochem.Mol.Biol. / Year: 2020
Title: Crystal structure of the N-terminal domain of ryanodine receptor from the honeybee, Apis mellifera.
Authors: Zhou, Y. / Wang, W. / Salauddin, N.M. / Lin, L. / You, M. / You, S. / Yuchi, Z.
History
DepositionJan 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 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
A: ryanodine receptor
B: ryanodine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3963
Polymers44,3712
Non-polymers241
Water36020
1
A: ryanodine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2102
Polymers22,1861
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-5 kcal/mol
Surface area8330 Å2
MethodPISA
2
B: ryanodine receptor


Theoretical massNumber of molelcules
Total (without water)22,1861
Polymers22,1861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.054, 75.363, 143.878
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 /


Mass: 22185.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apis mellifera (honey bee) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A088AV96, UniProt: A0A7M7R4R0*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.2 Å3/Da / Density % sol: 44.16 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium chloride hexahydrate, 34%-40% PEG 4000, 0.1 M Tris, pH 8.5-9.4
PH range: 8.5-9.4

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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: Jan 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.499→50 Å / Num. obs: 14282 / % possible obs: 99.8 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.054 / Rrim(I) all: 0.134 / Χ2: 0.762 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.545.40.6997100.8410.3220.7730.44698.7
2.54-2.595.50.6336820.9460.2870.6970.49999.4
2.59-2.645.80.6636770.8920.2990.7290.50998.8
2.64-2.695.80.6727050.870.3020.7390.79299.3
2.69-2.755.70.4957010.9340.2260.5460.48999.9
2.75-2.825.70.4377000.960.1970.4810.521100
2.82-2.8960.3956820.9690.1760.4340.511100
2.89-2.966.50.3167090.9710.1340.3440.543100
2.96-3.056.60.2837060.960.1190.3080.583100
3.05-3.156.50.2527010.9760.1070.2740.642100
3.15-3.266.50.2087240.9880.0880.2260.638100
3.26-3.396.50.1796840.9870.0760.1950.721100
3.39-3.556.10.1877150.9750.0830.2051.008100
3.55-3.735.90.137100.9870.0590.1430.894100
3.73-3.976.40.1167330.9880.0490.1261.061100
3.97-4.276.50.0847080.9940.0360.0911.041100
4.27-4.76.40.0777310.9940.0330.0841.085100
4.7-5.385.90.0757350.9960.0330.0821.083100
5.38-6.786.10.0767500.9960.0340.0840.946100
6.78-505.50.0778190.9970.0350.0851.02899.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3247refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y9V

5y9v


Resolution: 2.499→37.682 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 33.64
RfactorNum. reflection% reflection
Rfree0.2878 1360 10.04 %
Rwork0.2227 --
obs0.229 13540 94.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.45 Å2 / Biso mean: 56.1681 Å2 / Biso min: 29.93 Å2
Refinement stepCycle: final / Resolution: 2.499→37.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 1 20 2421
Biso mean--59.57 51.56 -
Num. residues----338
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4991-2.58840.39791160.2759104682
2.5884-2.6920.3331260.2746108487
2.692-2.81450.36651290.2557113890
2.8145-2.96280.29981300.2287118695
2.9628-3.14830.31141340.2398122797
3.1483-3.39130.31891370.2343124298
3.3913-3.73230.33651410.2218126499
3.7323-4.27170.2681420.2044128699
4.2717-5.37940.23781480.1841315100
5.3794-37.6820.25911570.24181392100

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