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- PDB-9d3f: Water and chloride as allosteric inhibitors in WNK kinase osmosensing -

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Basic information

Entry
Database: PDB / ID: 9d3f
TitleWater and chloride as allosteric inhibitors in WNK kinase osmosensing
ComponentsSerine/threonine-protein kinase WNK1
KeywordsTRANSFERASE / WNK1 / kinase / PEG400 / complex
Function / homology
Function and homology information


negative regulation of cell-cell adhesion mediated by integrin / lymphocyte migration into lymph node / chemokine (C-C motif) ligand 21 signaling pathway / monoatomic cation homeostasis / positive regulation of termination of RNA polymerase II transcription / negative regulation of pancreatic juice secretion / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / monoatomic ion homeostasis / positive regulation of mitotic cytokinesis / negative regulation of sodium ion transport ...negative regulation of cell-cell adhesion mediated by integrin / lymphocyte migration into lymph node / chemokine (C-C motif) ligand 21 signaling pathway / monoatomic cation homeostasis / positive regulation of termination of RNA polymerase II transcription / negative regulation of pancreatic juice secretion / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / monoatomic ion homeostasis / positive regulation of mitotic cytokinesis / negative regulation of sodium ion transport / positive regulation of potassium ion import across plasma membrane / regulation of mRNA export from nucleus / intracellular chloride ion homeostasis / negative regulation of heterotypic cell-cell adhesion / positive regulation of T cell chemotaxis / regulation of sodium ion transmembrane transport / potassium channel inhibitor activity / cellular response to chemokine / potassium ion homeostasis / negative regulation of leukocyte cell-cell adhesion / cellular hyperosmotic response / membraneless organelle assembly / cell volume homeostasis / regulation of monoatomic cation transmembrane transport / protein serine/threonine kinase inhibitor activity / intracellular membraneless organelle / positive regulation of systemic arterial blood pressure / protein kinase activator activity / negative regulation of protein localization to plasma membrane / phosphatase binding / regulation of sodium ion transport / monoatomic ion transport / negative regulation of protein ubiquitination / sodium ion transmembrane transport / negative regulation of autophagy / cellular response to calcium ion / GABA-ergic synapse / modulation of chemical synaptic transmission / molecular condensate scaffold activity / regulation of blood pressure / positive regulation of angiogenesis / mitotic spindle / positive regulation of canonical Wnt signaling pathway / T cell receptor signaling pathway / heart development / 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 / protein kinase binding / magnesium ion binding / signal transduction / protein-containing complex / ATP binding / nucleus / membrane / cytosol / 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 WNK1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAkella, R. / Goldsmith, E.J.
Funding support United States, 2items
OrganizationGrant numberCountry
Robert A. Welch FoundationI1128 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK110358 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 9, 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

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase WNK1


Theoretical massNumber of molelcules
Total (without water)33,5121
Polymers33,5121
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.323, 56.812, 65.281
Angle α, β, γ (deg.)90.000, 95.379, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein kinase WNK1 / Protein kinase lysine-deficient 1 / Protein kinase with no lysine 1


Mass: 33511.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Wnk1, Hsn2, Prkwnk1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9JIH7, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.11 Å3/Da / Density % sol: 41.74 % / Description: plates
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 400mM Potassium formate, 20% PEG3350, crystals soaked in 15% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Oct 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→42.774 Å / Num. obs: 18236 / % possible obs: 96 % / Redundancy: 7.6 % / Biso Wilson estimate: 18.5 Å2 / CC1/2: 0.76 / Net I/σ(I): 29.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.7 % / Num. unique obs: 900 / CC1/2: 0.55 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
HKL-3000722data reduction
HKL-3000722data scaling
MOLREP8.0.013phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.774 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.146 / SU ML: 0.117 / Cross valid method: FREE R-VALUE / ESU R: 0.223 / ESU R Free: 0.177
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2357 939 5.149 %
Rwork0.2044 17297 -
all0.206 --
obs-18236 95.828 %
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: 52.193 Å2
Baniso -1Baniso -2Baniso -3
1--0.024 Å2-0 Å20.025 Å2
2---0.12 Å2-0 Å2
3---0.137 Å2
Refinement stepCycle: LAST / Resolution: 2→42.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2135 0 0 145 2280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122175
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162116
X-RAY DIFFRACTIONr_angle_refined_deg0.2841.6632921
X-RAY DIFFRACTIONr_angle_other_deg0.1181.5784889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.9445263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.741516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.67810421
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.7511097
X-RAY DIFFRACTIONr_chiral_restr0.0360.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022503
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02495
X-RAY DIFFRACTIONr_nbd_refined0.230.2558
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2490.22030
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21084
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21136
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2118
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0680.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2480.213
X-RAY DIFFRACTIONr_nbd_other0.2420.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2120.214
X-RAY DIFFRACTIONr_mcbond_it4.4485.1741058
X-RAY DIFFRACTIONr_mcbond_other4.4465.1751058
X-RAY DIFFRACTIONr_mcangle_it6.5779.2911319
X-RAY DIFFRACTIONr_mcangle_other6.5839.2921320
X-RAY DIFFRACTIONr_scbond_it5.4155.851117
X-RAY DIFFRACTIONr_scbond_other5.4135.8531118
X-RAY DIFFRACTIONr_scangle_it8.48910.4611602
X-RAY DIFFRACTIONr_scangle_other8.48710.4621603
X-RAY DIFFRACTIONr_lrange_it12.36663.3799081
X-RAY DIFFRACTIONr_lrange_other12.38763.2929034
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
2-2.0520.283780.25812020.25913820.9380.95492.61940.201
2.052-2.1080.268690.2212670.22213840.9540.9796.53180.189
2.108-2.1690.223710.21111880.21113060.9560.97396.40120.186
2.169-2.2350.256660.19411680.19712830.9540.97796.18080.178
2.235-2.3090.25480.19611530.19812490.9670.97696.15690.18
2.309-2.3890.227700.18410980.18612160.9670.97896.05260.168
2.389-2.4790.237640.17110530.17411560.9680.98196.62630.161
2.479-2.580.183380.17110350.17211280.980.98295.12410.163
2.58-2.6940.251640.1839620.18710720.9640.9895.7090.175
2.694-2.8250.223420.1879530.18810270.9660.9896.88410.19
2.825-2.9770.2420.1979270.19710040.9750.97896.51390.202
2.977-3.1570.279420.1878550.1919220.9590.97997.28850.195
3.157-3.3740.286390.2057860.2098580.9420.97296.15380.216
3.374-3.6420.262490.2037330.2078280.960.97394.44440.218
3.642-3.9870.179310.1866660.1867460.9820.97893.43160.206
3.987-4.4530.179350.1786330.1786800.9750.9898.23530.198
4.453-5.1320.21330.1945610.1956130.9750.97696.90050.221
5.132-6.2630.316260.2584720.2625210.9390.96195.58540.298
6.263-8.7640.307130.2483610.254020.960.96293.03480.301
8.764-42.7740.216190.272180.2652460.9760.9696.34150.347

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