5W7T | pdb_00005w7t

STRUCTURE OF PHOSPHORYLATED WNK1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 
    0.227 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

A Phosphorylated Intermediate in the Activation of WNK Kinases.

Akella, R.Drozdz, M.A.Humphreys, J.M.Jiou, J.Durbacz, M.Z.Mohammed, Z.J.He, H.Liwocha, J.Sekulski, K.Goldsmith, E.J.

(2020) Biochemistry 59: 1747-1755

  • DOI: https://doi.org/10.1021/acs.biochem.0c00146
  • Primary Citation of Related Structures:  
    5W7T

  • PubMed Abstract: 

    WNK kinases autoactivate by autophosphorylation. Crystallography of the kinase domain of WNK1 phosphorylated on the primary activating site (pWNK1) in the presence of AMP-PNP reveals a well-ordered but inactive configuration. This new pWNK1 structure features specific and unique interactions of the phosphoserine, less hydration, and smaller cavities compared with those of unphosphorylated WNK1 (uWNK1). Because WNKs are activated by osmotic stress in cells, we addressed whether the structure was influenced directly by osmotic pressure. pWNK1 crystals formed in PEG3350 were soaked in the osmolyte sucrose. Suc-WNK1 crystals maintained X-ray diffraction, but the lattice constants and pWNK1 structure changed. Differences were found in the activation loop and helix C, common switch loci in kinase activation. On the basis of these structural changes, we tested for effects on in vitro activity of two WNKs, pWNK1 and pWNK3. The osmolyte PEG400 enhanced ATPase activity. Our data suggest multistage activation of WNKs.


  • Organizational Affiliation
    • Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8816, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase WNK1
A, B
277Rattus norvegicusMutation(s): 0 
Gene Names: Wnk1Hsn2Prkwnk1
EC: 2.7.11.1
UniProt
Find proteins for Q9JIH7 (Rattus norvegicus)
Explore Q9JIH7 
Go to UniProtKB:  Q9JIH7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JIH7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A, B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.175α = 90
b = 62.23β = 92.26
c = 120.899γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
American Heart AssociationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary
  • Version 1.4: 2025-08-06
    Changes: Database references