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- PDB-5o2c: Crystal structure of WNK3 kinase and CCT1 didomain in a unphospho... -

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Basic information

Entry
Database: PDB / ID: 5o2c
TitleCrystal structure of WNK3 kinase and CCT1 didomain in a unphosphorylated state
ComponentsSerine/threonine-protein kinase WNK3
KeywordsSTRUCTURAL GENOMICS / WNK3 / Structural Genomics Consortium / SGC
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 / negative regulation of sodium ion transport / positive regulation of potassium ion import across plasma membrane / regulation of calcium ion import / positive regulation of sodium ion transport / non-membrane-bounded organelle assembly / potassium channel inhibitor activity ...positive regulation of ion transmembrane transporter activity / negative regulation of pancreatic juice secretion / positive regulation of sodium ion transmembrane transporter activity / monoatomic ion homeostasis / negative regulation of sodium ion transport / positive regulation of potassium ion import across plasma membrane / regulation of calcium ion import / positive regulation of sodium ion transport / non-membrane-bounded organelle assembly / potassium channel inhibitor activity / positive regulation of calcium ion transport / cellular hyperosmotic response / osmosensory signaling pathway / regulation of monoatomic cation transmembrane transport / cell volume homeostasis / negative regulation of protein localization to plasma membrane / maintenance of blood-brain barrier / bicellular tight junction / positive regulation of peptidyl-threonine phosphorylation / molecular condensate scaffold activity / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / adherens junction / peptidyl-threonine phosphorylation / Stimuli-sensing channels / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / ATP binding / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Serine/threonine-protein kinase WNK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBartual, S.G. / Pinkas, D.M. / Bufton, J.C. / Kupinska, K. / Wang, D. / Chalk, R. / Berridge, G. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. ...Bartual, S.G. / Pinkas, D.M. / Bufton, J.C. / Kupinska, K. / Wang, D. / Chalk, R. / Berridge, G. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of WNK3 kinase and CCT1 didomain in a unphosphorylated state
Authors: Pinkas, D.M. / Daubner, G.M. / Bufton, J.C. / Bartual, S.G. / Sanvitale, C.E. / Alessi, D.R. / Bullock, A.
History
DepositionMay 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Serine/threonine-protein kinase WNK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0906
Polymers43,6151
Non-polymers4745
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint1 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.370, 64.080, 47.340
Angle α, β, γ (deg.)90.00, 97.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 43615.094 Da / Num. of mol.: 1 / Fragment: UNP residues 123-500
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WNK3, KIAA1566, PRKWNK3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9BYP7, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.87 Å3/Da / Density % sol: 57.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 18% PEG3350, 0.1 M Citrate pH 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.4→32.78 Å / Num. obs: 19384 / % possible obs: 99.6 % / Redundancy: 2.9 % / Biso Wilson estimate: 42.11 Å2 / Net I/σ(I): 6.3

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→24.47 Å / Cor.coef. Fo:Fc: 0.9048 / Cor.coef. Fo:Fc free: 0.8532 / SU R Cruickshank DPI: 0.295 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.293 / SU Rfree Blow DPI: 0.24 / SU Rfree Cruickshank DPI: 0.244
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 959 4.95 %RANDOM
Rwork0.1851 ---
obs0.1885 19365 99.46 %-
Displacement parametersBiso mean: 44.3 Å2
Baniso -1Baniso -2Baniso -3
1-11.4424 Å20 Å20.9077 Å2
2---20.8866 Å20 Å2
3---9.4442 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: 1 / Resolution: 2.4→24.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2948 0 31 117 3096
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013032HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.164072HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1106SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes427HARMONIC5
X-RAY DIFFRACTIONt_it3032HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion21.24
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion393SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3477SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.53 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2579 142 5.08 %
Rwork0.2188 2651 -
all0.2208 2793 -
obs--99.32 %

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