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- PDB-5d9h: Crystal structure of SPAK (STK39) dimer in the basal activity state -

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Basic information

Entry
Database: PDB / ID: 5d9h
TitleCrystal structure of SPAK (STK39) dimer in the basal activity state
ComponentsSTE20/SPS1-related proline-alanine-rich protein kinase
KeywordsTRANSFERASE / Kinase / Ste20 / Hypertension / stk39
Function / homology
Function and homology information


negative regulation of creatine transmembrane transporter activity / positive regulation of ion transmembrane transporter activity / negative regulation of pancreatic juice secretion / maintenance of lens transparency / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of potassium ion transmembrane transporter activity / monoatomic ion homeostasis / negative regulation of potassium ion transmembrane transport / intracellular chloride ion homeostasis / negative regulation of sodium ion transmembrane transporter activity ...negative regulation of creatine transmembrane transporter activity / positive regulation of ion transmembrane transporter activity / negative regulation of pancreatic juice secretion / maintenance of lens transparency / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of potassium ion transmembrane transporter activity / monoatomic ion homeostasis / negative regulation of potassium ion transmembrane transport / intracellular chloride ion homeostasis / negative regulation of sodium ion transmembrane transporter activity / positive regulation of T cell chemotaxis / cellular hypotonic response / cellular response to potassium ion / macrophage activation / positive regulation of potassium ion transport / cellular response to chemokine / positive regulation of p38MAPK cascade / extrinsic component of membrane / response to aldosterone / response to dietary excess / sodium ion transmembrane transport / peptidyl-threonine phosphorylation / regulation of blood pressure / cell body / cell cortex / kinase activity / regulation of inflammatory response / basolateral plasma membrane / peptidyl-serine phosphorylation / protein autophosphorylation / cytoskeleton / non-specific serine/threonine protein kinase / intracellular signal transduction / inflammatory response / apical plasma membrane / protein phosphorylation / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / protein kinase binding / signal transduction / nucleoplasm / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / STE20/SPS1-related proline-alanine-rich protein kinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsTaylor, C.A. / Juang, Y.C. / Goldsmith, E.J. / Cobb, M.H.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM53032 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK46993 United States
Welch FoundationI1143 United States
Welch FoundationI1128 United States
CitationJournal: Biochemistry / Year: 2015
Title: Domain-Swapping Switch Point in Ste20 Protein Kinase SPAK.
Authors: Taylor, C.A. / Juang, Y.C. / Earnest, S. / Sengupta, S. / Goldsmith, E.J. / Cobb, M.H.
History
DepositionAug 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STE20/SPS1-related proline-alanine-rich protein kinase
B: STE20/SPS1-related proline-alanine-rich protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,91011
Polymers78,3662
Non-polymers1,5439
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-101 kcal/mol
Surface area27170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.386, 56.105, 99.958
Angle α, β, γ (deg.)90.000, 108.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein STE20/SPS1-related proline-alanine-rich protein kinase / Ste-20-related kinase / Serine/threonine-protein kinase 39


Mass: 39183.246 Da / Num. of mol.: 2 / Fragment: UNP residues 63-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Stk39, Spak / Plasmid: pHis.parallel1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Z1W9, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4

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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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM MES, 150 mM ammonium sulfate, 18% PEG4000, 1:1 drop ratio

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→42.9 Å / Num. all: 38612 / Num. obs: 13658 / % possible obs: 85.6 % / Redundancy: 2.8 % / Biso Wilson estimate: 62.87 Å2 / Rmerge(I) obs: 0.069 / Χ2: 0.906 / Net I/σ(I): 15.1 / Num. measured all: 38612
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
3.1-3.20.4922.16770.78944.3
3.15-3.212.80.4886650.8398.2
3.21-3.272.90.4086960.80398.7
3.27-3.342.80.3216750.90898.7
3.34-3.412.90.2766800.8998.6
3.41-3.492.80.2666781.17798.1
3.49-3.582.90.1736960.90998.6
3.58-3.682.80.1676791.3298.1
3.68-3.782.80.1266830.89998.3
3.78-3.912.90.116671.24297.9
3.91-4.042.90.0916790.89197.7
4.04-4.212.90.0726750.82897.4
4.21-4.42.90.066900.86397.6
4.4-4.632.90.0576790.82997.6
4.63-4.922.80.0566810.84397
4.92-5.32.80.0556820.80997.4
5.3-5.832.80.0576840.78796.9
5.83-6.672.80.0536880.78896.6
6.67-8.42.80.056930.79196.7
8.4-502.70.0477110.92494.7

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
HKL-3000phasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→42.867 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 28.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1193 9.92 %Random
Rwork0.236 10839 --
obs0.2403 12032 85.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 213.04 Å2 / Biso mean: 76.7878 Å2 / Biso min: 19.02 Å2
Refinement stepCycle: final / Resolution: 3.1→42.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4569 0 113 0 4682
Biso mean--76.98 --
Num. residues----583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094736
X-RAY DIFFRACTIONf_angle_d1.1816403
X-RAY DIFFRACTIONf_chiral_restr0.057719
X-RAY DIFFRACTIONf_plane_restr0.005793
X-RAY DIFFRACTIONf_dihedral_angle_d13.5141789
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.22620.3877730.31362870146
3.2262-3.3730.39321020.2883938104067
3.373-3.55070.32681250.27281153127883
3.5507-3.77310.28711470.25941297144493
3.7731-4.06420.27191440.24781342148695
4.0642-4.47280.25521480.20851342149096
4.4728-5.11910.27411540.21441373152796
5.1191-6.4460.28751430.24761363150697
6.446-42.8710.19531570.21661403156095

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