[English] 日本語
Yorodumi
- PDB-9znm: WNK1/SA kinase domain in complex with potassium formate at 1 Angs... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9znm
TitleWNK1/SA kinase domain in complex with potassium formate at 1 Angstrom wavelength
ComponentsSerine/threonine-protein kinase WNK1
KeywordsSIGNALING PROTEIN / WNK1 kinase domain / potassium / inactive asymmetric dimer / inhibition
Function / homology
Function and homology information


negative regulation of cell-cell adhesion mediated by integrin / monoatomic cation homeostasis / chemokine (C-C motif) ligand 21 signaling pathway / lymphocyte migration into lymph node / 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 / negative regulation of small GTPase mediated signal transduction / negative regulation of sodium ion transport / monoatomic ion homeostasis ...negative regulation of cell-cell adhesion mediated by integrin / monoatomic cation homeostasis / chemokine (C-C motif) ligand 21 signaling pathway / lymphocyte migration into lymph node / 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 / negative regulation of small GTPase mediated signal transduction / negative regulation of sodium ion transport / monoatomic ion homeostasis / positive regulation of mitotic cytokinesis / intracellular membraneless organelle / positive regulation of potassium ion import across plasma membrane / negative regulation of heterotypic cell-cell adhesion / regulation of mRNA export from nucleus / intracellular chloride ion homeostasis / positive regulation of T cell chemotaxis / regulation of sodium ion transmembrane transport / cellular response to chemokine / negative regulation of leukocyte cell-cell adhesion / potassium ion homeostasis / cellular hyperosmotic response / membraneless organelle assembly / potassium channel inhibitor activity / cell volume homeostasis / regulation of monoatomic cation transmembrane transport / positive regulation of systemic arterial blood pressure / protein kinase activator activity / protein serine/threonine kinase inhibitor activity / negative regulation of protein localization to plasma membrane / phosphatase binding / regulation of sodium ion transport / monoatomic ion transport / negative regulation of protein ubiquitination / potassium ion transmembrane transport / cellular response to calcium ion / negative regulation of autophagy / sodium ion transmembrane transport / molecular condensate scaffold activity / modulation of chemical synaptic transmission / regulation of blood pressure / GABA-ergic synapse / positive regulation of angiogenesis / mitotic spindle / positive regulation of canonical Wnt signaling pathway / T cell receptor signaling pathway / heart development / protein phosphorylation / protein kinase activity / non-specific serine/threonine protein kinase / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / magnesium ion binding / signal transduction / protein-containing complex / ATP binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
: / : / WNK CCTL2 domain / Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / 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. ...: / : / WNK CCTL2 domain / Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / 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
Similarity search - Domain/homology
: / Serine/threonine-protein kinase WNK1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGoldsmith, E.J. / Akella, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK110358 United States
Robert A. Welch FoundationI-2100-20220331 United States
CitationJournal: Biochemistry / Year: 2026
Title: Structural Basis for Potassium Inhibition of WNK Kinases.
Authors: Goldsmith, E.J. / Pleinis, J.M. / Wagner, A. / Mykhaylyk, V. / Akella, R. / Humphreys, J.M. / He, H. / Norrell, L. / Morrison, D.E. / Rodan, A.R.
History
DepositionDec 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase WNK1
B: Serine/threonine-protein kinase WNK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,42115
Polymers66,5032
Non-polymers91813
Water4,468248
1
B: Serine/threonine-protein kinase WNK1
hetero molecules

A: Serine/threonine-protein kinase WNK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,42115
Polymers66,5032
Non-polymers91813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area4520 Å2
ΔGint-57 kcal/mol
Surface area25510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.250, 57.720, 65.605
Angle α, β, γ (deg.)89.00, 89.65, 89.22
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 33251.281 Da / Num. of mol.: 2 / Mutation: S382A
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

-
Non-polymers , 6 types, 261 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 50 mM Tris/HCl pH 7.4, 5 mM EDTA, 200 mM potassium formate, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 35704 / % possible obs: 92 % / Redundancy: 7.3 % / CC1/2: 0.986 / CC star: 0.997 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.041 / Rrim(I) all: 0.113 / Χ2: 1.888 / Net I/σ(I): 6.7 / Num. measured all: 261544
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.98-2.015.60.5318070.910.9760.2290.5780.50691.8
2.01-2.056.10.49817960.9380.9840.2080.5410.51492.4
2.05-2.096.40.45217780.9370.9840.1840.4880.58692.3
2.09-2.136.70.42418130.9550.9880.1710.4580.60192.3
2.13-2.1870.3817520.9650.9910.150.4090.62892.2
2.18-2.237.10.35317450.9710.9930.1380.3790.65290.3
2.23-2.297.20.3116680.9620.990.1220.3330.69386.2
2.29-2.357.50.27917940.9730.9930.1080.30.70891.6
2.35-2.427.70.25318120.9840.9960.0970.2710.73994
2.42-2.497.80.20818150.9890.9970.0790.2220.86193.4
2.49-2.587.70.18817980.990.9970.0720.2020.89393.1
2.58-2.697.50.16617980.9910.9980.0640.1781.02392.4
2.69-2.817.40.13416570.990.9970.0520.1441.21885.8
2.81-2.967.80.12318510.990.9980.0470.1321.30694.7
2.96-3.147.80.10918340.9930.9980.0420.1171.63694.4
3.14-3.397.80.09717930.9940.9990.0370.1042.19893.5
3.39-3.737.60.08717300.9950.9990.0330.0942.66589
3.73-4.2680.07818750.9950.9990.0290.0833.67796
4.26-5.377.80.06517720.9960.9990.0250.073.0391.3
5.37-507.90.0718160.9930.9980.0270.07511.39793.9

-
Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
HKL-3000data scaling
DENZOdata reduction
PDB_EXTRACTdata extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.96 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 24.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2258 1814 5.35 %
Rwork0.177 --
obs0.1797 33888 89.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→42.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4369 0 53 248 4670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074493
X-RAY DIFFRACTIONf_angle_d0.8826022
X-RAY DIFFRACTIONf_dihedral_angle_d15.4181720
X-RAY DIFFRACTIONf_chiral_restr0.054659
X-RAY DIFFRACTIONf_plane_restr0.008754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.31831320.22042455X-RAY DIFFRACTION89
2.05-2.110.2751440.20342492X-RAY DIFFRACTION90
2.11-2.180.24361470.19712410X-RAY DIFFRACTION89
2.18-2.260.2931110.19162425X-RAY DIFFRACTION87
2.26-2.350.23831400.1912328X-RAY DIFFRACTION84
2.35-2.460.2811310.19952538X-RAY DIFFRACTION92
2.46-2.590.26571400.19522489X-RAY DIFFRACTION91
2.59-2.750.26831450.19622469X-RAY DIFFRACTION89
2.75-2.960.24291470.19472413X-RAY DIFFRACTION88
2.96-3.260.25041580.18982527X-RAY DIFFRACTION92
3.26-3.730.19841040.16932447X-RAY DIFFRACTION88
3.73-4.70.19281430.14532617X-RAY DIFFRACTION94
4.7-42.960.19161720.16692464X-RAY DIFFRACTION90

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more