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- PDB-6cn9: Crystal structure of the Kinase domain of WNK1 -

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Basic information

Entry
Database: PDB / ID: 6cn9
TitleCrystal structure of the Kinase domain of WNK1
ComponentsSerine/threonine-protein kinase WNK1
KeywordsTRANSFERASE / kinase
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 / 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 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
Serine/threonine-protein kinase WNK1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsAkella, R. / Goldsmith, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Structure / Year: 2004
Title: Crystal structure of the kinase domain of WNK1, a kinase that causes a hereditary form of hypertension.
Authors: Min, X. / Lee, B.H. / Cobb, M.H. / Goldsmith, E.J.
History
DepositionMar 7, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionMar 27, 2019ID: 3FPQ
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 WNK1
B: Serine/threonine-protein kinase WNK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,67211
Polymers67,8392
Non-polymers8339
Water9,386521
1
A: Serine/threonine-protein kinase WNK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1964
Polymers33,9201
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase WNK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4767
Polymers33,9201
Non-polymers5576
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.308, 57.767, 65.657
Angle α, β, γ (deg.)91.32, 89.99, 90.88
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 33919.543 Da / Num. of mol.: 2 / Fragment: kinase domain (UNP residues 194-483)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Wnk1, Hsn2, Prkwnk1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9JIH7, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 24% PEG2000 MME, 300 mM sodium chloride, 100 mM HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97937 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Jan 1, 2006
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 50614 / % possible obs: 97.6 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.077 / Net I/av σ(I): 27.9 / Net I/σ(I): 27.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.144 / Num. unique obs: 49555 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→19 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.533 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21125 2534 5.1 %RANDOM
Rwork0.16109 ---
obs0.16364 47020 95.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.044 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.01 Å2
2--0.01 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.8→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4369 0 53 521 4943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194503
X-RAY DIFFRACTIONr_bond_other_d0.0020.024337
X-RAY DIFFRACTIONr_angle_refined_deg1.9651.9886036
X-RAY DIFFRACTIONr_angle_other_deg1.099310072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3445543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9623.571196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37115811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2291532
X-RAY DIFFRACTIONr_chiral_restr0.1210.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024836
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02924
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4982.4212172
X-RAY DIFFRACTIONr_mcbond_other2.4982.4182171
X-RAY DIFFRACTIONr_mcangle_it3.4823.622712
X-RAY DIFFRACTIONr_mcangle_other3.4823.6232713
X-RAY DIFFRACTIONr_scbond_it3.9522.9252331
X-RAY DIFFRACTIONr_scbond_other3.8592.9192327
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7194.173318
X-RAY DIFFRACTIONr_long_range_B_refined7.54230.6765283
X-RAY DIFFRACTIONr_long_range_B_other7.48530.3895236
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 182 -
Rwork0.187 3268 -
obs--90.1 %

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