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- PDB-2lru: Solution Structure of the WNK1 Autoinhibitory Domain -

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Basic information

Entry
Database: PDB / ID: 2lru
TitleSolution Structure of the WNK1 Autoinhibitory Domain
ComponentsSerine/threonine-protein kinase WNK1
KeywordsTRANSFERASE / autoinhibitory domain / PF2 domain
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 / 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 ...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 / 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 / potassium channel inhibitor activity / potassium ion homeostasis / cellular hyperosmotic response / cellular response to chemokine / protein serine/threonine kinase inhibitor activity / negative regulation of leukocyte cell-cell adhesion / regulation of monoatomic cation transmembrane transport / cell volume homeostasis / negative regulation of protein localization to plasma membrane / intracellular non-membrane-bounded organelle / protein kinase activator activity / sodium ion transmembrane transport / GABA-ergic synapse / phosphatase binding / monoatomic ion transport / regulation of sodium ion transport / negative regulation of protein ubiquitination / cellular response to calcium ion / molecular condensate scaffold activity / negative regulation of autophagy / modulation of chemical synaptic transmission / mitotic spindle / regulation of blood pressure / positive regulation of canonical Wnt signaling pathway / positive regulation of angiogenesis / 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 / 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
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailsclosest to the average, model 1
AuthorsMoon, T.M. / Correa, F. / Gardner, K.H. / Goldsmith, E.J.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Solution Structure of the WNK1 Autoinhibitory Domain, a WNK-Specific PF2 Domain.
Authors: Moon, T.M. / Correa, F. / Kinch, L.N. / Piala, A.T. / Gardner, K.H. / Goldsmith, E.J.
History
DepositionApr 13, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Apr 24, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase WNK1


Theoretical massNumber of molelcules
Total (without water)11,3591
Polymers11,3591
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 11358.877 Da / Num. of mol.: 1 / Fragment: UNP residues 480-572
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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D (H)CCH-TOCSY
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D H(CCO)NH
1713D C(CO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.65 mM [U-100% 13C; U-100% 15N] WNKAI, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.65 mM / Component: WNKAI-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.010 / pH: 6.5 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: The authors state that two protons (TYR516 hydroxyl, CYS 547 backbone amide) are clashing in 1 model of the 20, and are close in 6/20. While we have not been able to directly assign the ...Details: The authors state that two protons (TYR516 hydroxyl, CYS 547 backbone amide) are clashing in 1 model of the 20, and are close in 6/20. While we have not been able to directly assign the chemical shifts of that hydroxyl proton given the difficulties of exchange at this site, we believe that our existing NMR data are consistent with arrangement indicating a likely H-bond between the CYS 547 amide proton and TYR 516 hydroxyl oxygen.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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