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- PDB-4pwn: Crystal structure of Active WNK1 kinase -

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Basic information

Entry
Database: PDB / ID: 4pwn
TitleCrystal structure of Active WNK1 kinase
ComponentsSerine/threonine-protein kinase WNK1
KeywordsTRANSFERASE / kinase / WNK1 / Ser/Thr protein kinase / Serine/Threonine kinase / ATP-binding / phosphorylation
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 / negative regulation of small GTPase mediated signal transduction / 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 / negative regulation of small GTPase mediated signal transduction / positive regulation of mitotic cytokinesis / negative regulation of sodium ion transport / 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 / 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 / intracellular membraneless organelle / positive regulation of systemic arterial blood pressure / protein kinase activator activity / negative regulation of protein localization to plasma membrane / neuron development / phosphatase binding / regulation of sodium ion transport / monoatomic ion transport / negative regulation of protein ubiquitination / sodium ion transmembrane transport / negative regulation of autophagy / molecular condensate scaffold activity / Stimuli-sensing channels / positive regulation of angiogenesis / mitotic spindle / positive regulation of canonical Wnt signaling pathway / T cell receptor signaling pathway / heart development / 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 / protein kinase binding / signal transduction / protein-containing complex / ATP binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / WNK CCTL2 domain / : / Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site ...: / WNK CCTL2 domain / : / Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Serine/threonine-protein kinase WNK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsPiala, A. / Moon, T. / Akella, T. / He, H. / Cobbm, M.H. / Goldsmith, E.
CitationJournal: Sci.Signal. / Year: 2014
Title: Chloride Sensing by WNK1 Involves Inhibition of Autophosphorylation.
Authors: Piala, A.T. / Moon, T.M. / Akella, R. / He, H. / Cobb, M.H. / Goldsmith, E.J.
History
DepositionMar 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase WNK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6342
Polymers31,5391
Non-polymers951
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.737, 64.226, 42.082
Angle α, β, γ (deg.)90.00, 92.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein kinase WNK1 / Erythrocyte 65 kDa protein / p65 / Kinase deficient protein / Protein kinase lysine-deficient 1 / ...Erythrocyte 65 kDa protein / p65 / Kinase deficient protein / Protein kinase lysine-deficient 1 / Protein kinase with no lysine 1 / hWNK1


Mass: 31538.545 Da / Num. of mol.: 1 / Fragment: Serine/Threonine Protein kinase WNK1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WNK1, HSN2, KDP, KIAA0344, PRKWNK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H4A3, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.35M potassium phosphate, 19% PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→35.18 Å / Num. all: 75996 / Num. obs: 19568 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 30.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3FPQ

3fpq
PDB Unreleased entry


Resolution: 1.84→35.18 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.651 / SU ML: 0.159 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.195 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27363 1054 5.1 %RANDOM
Rwork0.22881 ---
obs0.23114 19568 98.99 %-
all-75996 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.493 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20.02 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.84→35.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 5 234 2215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192017
X-RAY DIFFRACTIONr_bond_other_d0.0010.021936
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.9692712
X-RAY DIFFRACTIONr_angle_other_deg0.80934471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5415241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83924.1392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51315380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0031512
X-RAY DIFFRACTIONr_chiral_restr0.0840.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022208
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02448
X-RAY DIFFRACTIONr_mcbond_it1.7242.823976
X-RAY DIFFRACTIONr_mcbond_other1.7232.821975
X-RAY DIFFRACTIONr_mcangle_it2.7634.2111213
X-RAY DIFFRACTIONr_mcangle_other2.7624.2141214
X-RAY DIFFRACTIONr_scbond_it1.7553.091041
X-RAY DIFFRACTIONr_scbond_other1.743.0811035
X-RAY DIFFRACTIONr_scangle_other2.8824.5371493
X-RAY DIFFRACTIONr_long_range_B_refined8.3325.442551
X-RAY DIFFRACTIONr_long_range_B_other8.00924.0752442
LS refinement shellResolution: 1.837→1.885 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 70 -
Rwork0.305 1306 -
obs--91.43 %
Refinement TLS params.Method: refined / Origin x: 13.4357 Å / Origin y: -0.1921 Å / Origin z: 11.6164 Å
111213212223313233
T0.127 Å20.0212 Å20.0251 Å2-0.1184 Å20.0096 Å2--0.0224 Å2
L2.8787 °2-2.3947 °2-0.2146 °2-4.1678 °20.5741 °2--0.4805 °2
S0.2476 Å °0.2374 Å °0.1758 Å °-0.3007 Å °-0.1802 Å °-0.195 Å °-0.0074 Å °-0.0058 Å °-0.0674 Å °

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