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Basic information

Entry
Database: PDB / ID: 2v3s
TitleStructural insights into the recognition of substrates and activators by the OSR1 kinase
Components
  • SERINE/THREONINE-PROTEIN KINASE OSR1
  • SERINE/THREONINE-PROTEIN KINASE WNK4
KeywordsTRANSFERASE / ATP-BINDING / KINASE / MAGNESIUM / METAL-BINDING / NUCLEOTIDE-BINDING / PHOSPHORYLATION / POLYMORPHISM / SERINE/THREONINE-PROTEIN KINASE
Function / homology
Function and homology information


distal tubule morphogenesis / aldosterone secretion / chemokine (C-C motif) ligand 21 signaling pathway / renal sodium ion transport / regulation of potassium ion export across plasma membrane / negative regulation of pancreatic juice secretion / chemokine (C-X-C motif) ligand 12 signaling pathway / monoatomic ion homeostasis / negative regulation of sodium ion transport / negative regulation of potassium ion transmembrane transport ...distal tubule morphogenesis / aldosterone secretion / chemokine (C-C motif) ligand 21 signaling pathway / renal sodium ion transport / regulation of potassium ion export across plasma membrane / negative regulation of pancreatic juice secretion / chemokine (C-X-C motif) ligand 12 signaling pathway / monoatomic ion homeostasis / negative regulation of sodium ion transport / negative regulation of potassium ion transmembrane transport / intracellular chloride ion homeostasis / renal sodium ion absorption / positive regulation of T cell chemotaxis / cellular hypotonic response / macrophage activation / cellular response to chemokine / osmosensory signaling pathway / cellular hyperosmotic response / cell volume homeostasis / chloride transport / chloride ion binding / ion channel inhibitor activity / response to dietary excess / bicellular tight junction / negative regulation of protein localization to plasma membrane / calcium ion homeostasis / potassium ion transmembrane transport / sodium ion transmembrane transport / peptidyl-threonine phosphorylation / ERK1 and ERK2 cascade / regulation of blood pressure / Stimuli-sensing channels / intracellular protein localization / cellular response to xenobiotic stimulus / cell body / protein autophosphorylation / gene expression / response to oxidative stress / 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 / inflammatory response / response to xenobiotic stimulus / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / magnesium ion binding / signal transduction / protein-containing complex / extracellular exosome / ATP binding / identical protein binding / membrane / 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) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...: / 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) / 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, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Serine/threonine-protein kinase OSR1 / Serine/threonine-protein kinase WNK4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVilla, F. / Goebel, J. / Rafiqi, F.H. / Deak, M. / Thastrup, J. / Alessi, D.R. / van Aalten, D.M.F.
CitationJournal: Embo Rep. / Year: 2007
Title: Structural Insights Into the Recognition of Substrates and Activators by the Osr1 Kinase
Authors: Villa, F. / Goebel, J. / Rafiqi, F.H. / Deak, M. / Thastrup, J. / Alessi, D.R. / Van Aalten, D.M.F.
History
DepositionJun 21, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE OSR1
B: SERINE/THREONINE-PROTEIN KINASE OSR1
C: SERINE/THREONINE-PROTEIN KINASE WNK4
D: SERINE/THREONINE-PROTEIN KINASE WNK4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1145
Polymers22,0554
Non-polymers591
Water5,873326
1
A: SERINE/THREONINE-PROTEIN KINASE OSR1
D: SERINE/THREONINE-PROTEIN KINASE WNK4


Theoretical massNumber of molelcules
Total (without water)11,0272
Polymers11,0272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint74.8 kcal/mol
Surface area7110 Å2
MethodPQS
2
B: SERINE/THREONINE-PROTEIN KINASE OSR1
C: SERINE/THREONINE-PROTEIN KINASE WNK4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0863
Polymers11,0272
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-2.8 kcal/mol
Surface area7250 Å2
MethodPQS
Unit cell
Length a, b, c (Å)31.469, 52.754, 59.271
Angle α, β, γ (deg.)90.00, 103.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE OSR1 / OXIDATIVE STRESS-RESPONSIVE 1 PROTEIN


Mass: 10319.632 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O95747, non-specific serine/threonine protein kinase
#2: Protein/peptide SERINE/THREONINE-PROTEIN KINASE WNK4 / PROTEIN KINASE WITH NO LYSINE 4 / PROTEIN KINASE LYSINE-DEFICIENT 4


Mass: 707.798 Da / Num. of mol.: 2 / Fragment: RESIDUES 1015-1020 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
References: UniProt: Q96J92, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O
Compound detailsREGULATES DOWNSTREAM KINASES IN RESPONSE TO ENVIRONMENTAL STRESS. MAY ALSO HAVE A FUNCTION IN ...REGULATES DOWNSTREAM KINASES IN RESPONSE TO ENVIRONMENTAL STRESS. MAY ALSO HAVE A FUNCTION IN REGULATING THE ACTIN CYTOSKELETON.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 33 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 20989 / % possible obs: 91 % / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 33.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.387 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 634 3.2 %RANDOM
Rwork0.198 ---
obs0.2 19179 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.01 Å2
2--0.75 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1528 0 4 326 1858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221550
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.9932085
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.4455199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.72824.49369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70415278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2131514
X-RAY DIFFRACTIONr_chiral_restr0.1180.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021160
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.2757
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21062
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3540.2227
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.261
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9081.51030
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53621603
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.283559
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7744.5482
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.553 50
Rwork0.466 1361

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