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- PDB-4q2a: WNK1: A chloride sensor via autophosphorylation -

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Basic information

Entry
Database: PDB / ID: 4q2a
TitleWNK1: A chloride sensor via autophosphorylation
ComponentsSerine/threonine-protein kinase WNK1
KeywordsTRANSFERASE / protein serine/threonine kinase / kinase / ATP-binding / unphosphorylated
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 / 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 cation homeostasis / positive regulation of mitotic cytokinesis / negative regulation of sodium ion transport / positive regulation of potassium ion import across plasma membrane ...negative regulation of cell-cell adhesion mediated by integrin / lymphocyte migration into lymph node / chemokine (C-C motif) ligand 21 signaling pathway / 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 cation homeostasis / positive regulation of mitotic cytokinesis / negative regulation of sodium ion transport / positive regulation of potassium ion import across plasma membrane / monoatomic ion homeostasis / regulation of mRNA export from nucleus / intracellular chloride ion homeostasis / negative regulation of heterotypic cell-cell adhesion / positive regulation of T cell chemotaxis / positive regulation of systemic arterial blood pressure / regulation of sodium ion transmembrane transport / membraneless organelle assembly / potassium channel inhibitor activity / cellular response to chemokine / potassium ion homeostasis / negative regulation of leukocyte cell-cell adhesion / cellular hyperosmotic response / protein serine/threonine kinase inhibitor activity / regulation of monoatomic cation transmembrane transport / cell volume homeostasis / intracellular membraneless organelle / protein kinase activator activity / phosphatase binding / negative regulation of protein localization to plasma membrane / sodium ion transmembrane transport / GABA-ergic synapse / regulation of sodium ion transport / monoatomic ion transport / negative regulation of protein ubiquitination / cellular response to calcium ion / negative regulation of autophagy / molecular condensate scaffold activity / modulation of chemical synaptic transmission / mitotic spindle / regulation of blood pressure / positive regulation of angiogenesis / positive regulation of canonical Wnt signaling pathway / heart development / T cell receptor signaling pathway / 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 / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / 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 kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / 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 / 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
BROMIDE ION / Serine/threonine-protein kinase WNK1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å
AuthorsPiala, A. / Moon, T. / Akella, R. / He, H. / Cobb, 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
DepositionApr 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,2022
Polymers33,1221
Non-polymers801
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.005, 58.304, 65.043
Angle α, β, γ (deg.)90.00, 91.35, 90.00
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: 33122.168 Da / Num. of mol.: 1 / Fragment: kinase domain (UNP residues 194-480) / Mutation: S382A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Hsn2, Prkwnk1, Wnk1 / Plasmid: PHIS Parallel / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9JIH7, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.18 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 26% PEG2000 MME, 300 mM sodium bromide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.91997 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2012 / Details: mirrors
RadiationMonochromator: Rosenbaum-Rock double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91997 Å / Relative weight: 1
ReflectionResolution: 3.5→43.409 Å / Num. all: 3680 / Num. obs: 3290 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.288 / Net I/σ(I): 44.3
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 4.3 / % possible all: 96.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 3FPQ

3fpq
PDB Unreleased entry


Resolution: 3.5→43.409 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.88 / SU B: 87.762 / SU ML: 0.633 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.882 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29743 364 10 %RANDOM
Rwork0.2428 ---
obs0.24827 3290 99.37 %-
all-3680 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 114.639 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0 Å2-0.05 Å2
2--0.58 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 3.5→43.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 1 9 2190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0192222
X-RAY DIFFRACTIONr_angle_refined_deg0.7531.9692985
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3695270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.09623.50597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21415431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2281516
X-RAY DIFFRACTIONr_chiral_restr0.0490.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211628
X-RAY DIFFRACTIONr_mcbond_it0.7187.3111083
X-RAY DIFFRACTIONr_mcangle_it1.3310.9671352
X-RAY DIFFRACTIONr_scbond_it0.5377.3551139
X-RAY DIFFRACTIONr_long_range_B_refined4.58160.3413326
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 25 -
Rwork0.265 233 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 13.3208 Å / Origin y: 0.3161 Å / Origin z: 17.265 Å
111213212223313233
T0.1317 Å2-0.0102 Å20.0043 Å2-0.1224 Å2-0.0304 Å2--0.0737 Å2
L4.9451 °2-0.0024 °20.7294 °2-7.0864 °21.9396 °2--5.879 °2
S0.0176 Å °0.5792 Å °-0.28 Å °-0.96 Å °0.0721 Å °-0.0478 Å °-0.3181 Å °-0.1995 Å °-0.0897 Å °

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