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- PDB-6fbk: Crystal structure of the human WNK2 CCT-like 1 domain in complex ... -

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Basic information

Entry
Database: PDB / ID: 6fbk
TitleCrystal structure of the human WNK2 CCT-like 1 domain in complex with a WNK1 RFXV peptide
Components
  • Serine/threonine-protein kinase WNK1
  • Serine/threonine-protein kinase WNK2
KeywordsPEPTIDE BINDING PROTEIN / WNK2 / CCT Domain / AI domain / RFXV motif binding
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 / positive regulation of sodium ion transmembrane transporter activity / monoatomic cation homeostasis / negative regulation of pancreatic juice secretion / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / positive regulation of mitotic cytokinesis / monoatomic ion homeostasis ...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 / positive regulation of sodium ion transmembrane transporter activity / monoatomic cation homeostasis / negative regulation of pancreatic juice secretion / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / positive regulation of mitotic cytokinesis / monoatomic ion homeostasis / negative regulation of sodium ion transport / positive regulation of potassium ion import across plasma membrane / regulation of mRNA export from nucleus / regulation of sodium ion transmembrane transport / intracellular chloride ion homeostasis / negative regulation of heterotypic cell-cell adhesion / non-membrane-bounded organelle assembly / positive regulation of T cell chemotaxis / positive regulation of systemic arterial blood pressure / chloride channel inhibitor activity / potassium channel inhibitor activity / potassium ion homeostasis / cellular hyperosmotic response / cellular response to chemokine / negative regulation of leukocyte cell-cell adhesion / regulation of monoatomic cation transmembrane transport / cell volume homeostasis / negative regulation of protein localization to plasma membrane / negative regulation of GTPase activity / intracellular non-membrane-bounded organelle / protein kinase activator activity / sodium ion transmembrane transport / neuron development / phosphatase binding / monoatomic ion transport / regulation of sodium ion transport / negative regulation of protein ubiquitination / molecular condensate scaffold activity / negative regulation of autophagy / peptidyl-threonine phosphorylation / negative regulation of ERK1 and ERK2 cascade / Stimuli-sensing channels / mitotic spindle / positive regulation of canonical Wnt signaling pathway / positive regulation of angiogenesis / heart development / T cell receptor signaling pathway / peptidyl-serine phosphorylation / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / negative regulation of cell population proliferation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / signal transduction / protein-containing complex / ATP binding / membrane / nucleus / plasma 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 / Roll / Protein kinase domain profile. ...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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase WNK1 / Serine/threonine-protein kinase WNK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.743 Å
AuthorsPinkas, D.M. / Bufton, J.C. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.N.
CitationJournal: To Be Published
Title: Crystal structure of the human WNK2 CCT-like 1 domain in complex with a WNK1 RFXV peptide
Authors: Pinkas, D.M. / Bufton, J.C. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
History
DepositionDec 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 WNK2
P: Serine/threonine-protein kinase WNK1


Theoretical massNumber of molelcules
Total (without water)13,9512
Polymers13,9512
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-4 kcal/mol
Surface area6180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.047, 78.047, 37.736
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Serine/threonine-protein kinase WNK2 / Antigen NY-CO-43 / Protein kinase lysine-deficient 2 / Protein kinase with no lysine 2 / ...Antigen NY-CO-43 / Protein kinase lysine-deficient 2 / Protein kinase with no lysine 2 / Serologically defined colon cancer antigen 43


Mass: 11340.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WNK2, KIAA1760, PRKWNK2, SDCCAG43, P/OKcl.13 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: Q9Y3S1, non-specific serine/threonine protein kinase
#2: Protein/peptide 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: 2610.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9H4A3, non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 293 K / Method: vapor diffusion / pH: 7.5
Details: 20% PEG3350 -- 10% ethylene glycol -- 0.2M sodium fluoride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.74→55.3 Å / Num. obs: 11689 / % possible obs: 99.3 % / Redundancy: 6.5 % / Net I/σ(I): 20.7
Reflection shellResolution: 1.743→1.773 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ELM

6elm


Resolution: 1.743→33.973 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 50.6
Details: Refinement R factors are higher than expected for resolution and diffraction images show diffuse spots between the indexed spots that were not able to be integrated. Nevertheless, the structure appears correct.
RfactorNum. reflection% reflection
Rfree0.3341 551 4.72 %
Rwork0.2844 --
obs0.2869 11674 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.743→33.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms760 0 0 14 774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008771
X-RAY DIFFRACTIONf_angle_d0.8741045
X-RAY DIFFRACTIONf_dihedral_angle_d23.092460
X-RAY DIFFRACTIONf_chiral_restr0.054124
X-RAY DIFFRACTIONf_plane_restr0.006135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7429-1.91830.44661450.46192778X-RAY DIFFRACTION100
1.9183-2.19580.45511220.3912706X-RAY DIFFRACTION97
2.1958-2.76630.44411470.37652772X-RAY DIFFRACTION100
2.7663-33.97970.29011370.2392867X-RAY DIFFRACTION100

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