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- PDB-9d7q: Water and chloride as allosteric inhibitors in WNK kinase osmosensing -

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Basic information

Entry
Database: PDB / ID: 9d7q
TitleWater and chloride as allosteric inhibitors in WNK kinase osmosensing
ComponentsSerine/threonine-protein kinase WNK3
KeywordsTRANSFERASE / WNK / kinase / water / allostery / autophosphorylation / osmosensing / WNK1 / WNK3 / mass spectrometry
Function / homology
Function and homology information


positive regulation of ion transmembrane transporter activity / negative regulation of pancreatic juice secretion / positive regulation of sodium ion transmembrane transporter activity / monoatomic ion homeostasis / regulation of calcium ion import / positive regulation of sodium ion transport / osmosensory signaling pathway / positive regulation of calcium ion transport / cellular hyperosmotic response / membraneless organelle assembly ...positive regulation of ion transmembrane transporter activity / negative regulation of pancreatic juice secretion / positive regulation of sodium ion transmembrane transporter activity / monoatomic ion homeostasis / regulation of calcium ion import / positive regulation of sodium ion transport / osmosensory signaling pathway / positive regulation of calcium ion transport / cellular hyperosmotic response / membraneless organelle assembly / cell volume homeostasis / regulation of monoatomic cation transmembrane transport / positive regulation of peptidyl-threonine phosphorylation / maintenance of blood-brain barrier / bicellular tight junction / negative regulation of protein localization to plasma membrane / peptidyl-threonine phosphorylation / protein localization to plasma membrane / adherens junction / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / Stimuli-sensing channels / protein autophosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / negative regulation of apoptotic process / ATP binding / cytoplasm
Similarity search - Function
: / Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase WNK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.301 Å
AuthorsAkella, R. / Goldsmith, E.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK110358 United States
Robert A. Welch FoundationI1128 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP190421 United States
CitationJournal: Elife / Year: 2024
Title: Water and chloride as allosteric inhibitors in WNK kinase osmosensing.
Authors: Teixeira, L.R. / Akella, R. / Humphreys, J.M. / He, H. / Goldsmith, E.J.
History
DepositionAug 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase WNK3
B: Serine/threonine-protein kinase WNK3


Theoretical massNumber of molelcules
Total (without water)64,1282
Polymers64,1282
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-24 kcal/mol
Surface area27380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.170, 113.596, 67.524
Angle α, β, γ (deg.)90.000, 101.359, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein kinase WNK3 / Protein kinase lysine-deficient 3 / Protein kinase with no lysine 3


Mass: 32064.158 Da / Num. of mol.: 2 / Mutation: E314A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WNK3, KIAA1566, PRKWNK3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9BYP7, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.95 Å3/Da / Density % sol: 58.36 % / Description: plate
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 8% Tacsimate, 10% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.3→43.107 Å / Num. obs: 7872 / % possible obs: 75 % / Redundancy: 5.2 % / CC1/2: 0.96 / Net I/σ(I): 9.8
Reflection shellResolution: 3.3→3.36 Å / Num. unique obs: 50 / CC1/2: 0.6 / % possible all: 55

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.301→43.107 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.839 / SU B: 33.403 / SU ML: 0.519 / Cross valid method: FREE R-VALUE / ESU R Free: 0.778 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2698 372 4.726 %
Rwork0.1771 7500 -
all0.181 --
obs-7872 70.036 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 87.08 Å2
Baniso -1Baniso -2Baniso -3
1-3.357 Å20 Å20.722 Å2
2---1.099 Å20 Å2
3----2.358 Å2
Refinement stepCycle: LAST / Resolution: 3.301→43.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4263 0 0 109 4372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0124349
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.8545849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4415528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.002529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.110828
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.38910190
X-RAY DIFFRACTIONr_chiral_restr0.1160.2645
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023212
X-RAY DIFFRACTIONr_nbd_refined0.2470.22009
X-RAY DIFFRACTIONr_nbtor_refined0.3170.22984
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2163
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2360.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1320.24
X-RAY DIFFRACTIONr_mcbond_it7.138.2862122
X-RAY DIFFRACTIONr_mcangle_it11.75114.8672646
X-RAY DIFFRACTIONr_scbond_it8.5499.1252227
X-RAY DIFFRACTIONr_scangle_it13.91416.4243203
X-RAY DIFFRACTIONr_lrange_it22.35103.13218108
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.301-3.3860.41560.2981460.3028430.9670.95318.03080.287
3.386-3.4780.28580.2962330.2967840.9340.94730.73980.268
3.478-3.5780.499120.2473020.2547960.9070.96339.44720.216
3.578-3.6870.31220.2143430.2197410.9460.9749.25780.182
3.687-3.8070.218170.1874100.1897340.9640.97758.17440.158
3.807-3.940.223190.24500.2017150.9740.97565.59440.172
3.94-4.0870.315260.1994640.2056650.9280.97373.68420.166
4.087-4.2530.29240.1755210.1796880.9480.97979.21510.147
4.253-4.440.307260.1865000.1926260.9530.97884.02560.162
4.44-4.6540.269280.164950.1666070.9410.98386.16150.14
4.654-4.9030.22270.174980.1735760.9660.98191.14580.151
4.903-5.1960.339250.1645160.1725580.930.98296.95340.153
5.196-5.5490.264360.184730.1865090.9660.981000.165
5.549-5.9850.25180.1824560.1854760.9640.98199.57980.17
5.985-6.5440.334220.1734310.184580.9480.9898.90830.161
6.544-7.2950.253220.1633670.1684010.9690.98397.00750.162
7.295-8.3840.199100.1383370.143650.9710.98995.06850.168
8.384-10.1720.2190.1372290.143000.9870.98779.33330.165
10.172-14.0010.16180.1271900.1282380.9870.99183.19330.163
14.001-43.1070.23170.2271390.2271540.9710.96594.80520.237

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