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- PDB-5o26: Crystal structure of WNK3 kinase domain in a diphosphorylated sta... -

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Basic information

Entry
Database: PDB / ID: 5o26
TitleCrystal structure of WNK3 kinase domain in a diphosphorylated state and in complex with AMP-PNP/Mg2+
ComponentsSerine/threonine-protein kinase WNK3
KeywordsSTRUCTURAL GENOMICS / WNK3
Function / homology
Function and homology information


positive regulation of ion transmembrane transporter activity / negative regulation of pancreatic juice secretion / positive regulation of sodium ion transmembrane transporter activity / monoatomic ion homeostasis / regulation of calcium ion import / positive regulation of sodium ion transport / osmosensory signaling pathway / positive regulation of calcium ion transport / cellular hyperosmotic response / membraneless organelle assembly ...positive regulation of ion transmembrane transporter activity / negative regulation of pancreatic juice secretion / positive regulation of sodium ion transmembrane transporter activity / monoatomic ion homeostasis / regulation of calcium ion import / positive regulation of sodium ion transport / osmosensory signaling pathway / positive regulation of calcium ion transport / cellular hyperosmotic response / membraneless organelle assembly / cell volume homeostasis / regulation of monoatomic cation transmembrane transport / positive regulation of peptidyl-threonine phosphorylation / maintenance of blood-brain barrier / bicellular tight junction / negative regulation of protein localization to plasma membrane / peptidyl-threonine phosphorylation / protein localization to plasma membrane / adherens junction / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / Stimuli-sensing channels / protein autophosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / negative regulation of apoptotic process / ATP binding / cytoplasm
Similarity search - Function
: / Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...: / Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase WNK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.379 Å
AuthorsPinkas, D.M. / Bufton, J.C. / Newman, J.A. / Kopec, J. / Borkowska, O. / Chalk, R. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. ...Pinkas, D.M. / Bufton, J.C. / Newman, J.A. / Kopec, J. / Borkowska, O. / Chalk, R. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
CitationJournal: To Be Published
Title: Crystal structure of WNK3 kinase domain in a diphosphorylated state and in complex with AMP-PNP/Mg2+
Authors: Pinkas, D.M. / Daubner, G.M. / Bufton, J.C. / Bartual, S.G. / Sanvitale, C.E. / Alessi, D.R. / Bullock, A.
History
DepositionMay 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 2.0Oct 31, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.label_seq_id / _entity.formula_weight ..._atom_site.label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.seq_align_end
Revision 2.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase WNK3
B: Serine/threonine-protein kinase WNK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5439
Polymers65,3712
Non-polymers1,1727
Water2,972165
1
A: Serine/threonine-protein kinase WNK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3035
Polymers32,6861
Non-polymers6174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase WNK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2414
Polymers32,6861
Non-polymers5553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.163, 56.400, 71.236
Angle α, β, γ (deg.)79.79, 80.73, 90.00
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Serine/threonine-protein kinase WNK3 / Protein kinase lysine-deficient 3 / Protein kinase with no lysine 3


Mass: 32685.715 Da / Num. of mol.: 2 / Fragment: UNP residues 132-414
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WNK3, KIAA1566, PRKWNK3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9BYP7, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG3350, 0.1M bis-tris pH 5.5

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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 / Detector: PIXEL / Date: Apr 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.379→55.483 Å / Num. obs: 21510 / % possible obs: 98 % / Redundancy: 2 % / Net I/σ(I): 4.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.379→47.657 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 29.03
RfactorNum. reflection% reflection
Rfree0.2781 1083 5.04 %
Rwork0.2284 --
obs0.231 21503 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.379→47.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4248 0 70 165 4483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024411
X-RAY DIFFRACTIONf_angle_d0.485985
X-RAY DIFFRACTIONf_dihedral_angle_d16.5812631
X-RAY DIFFRACTIONf_chiral_restr0.041671
X-RAY DIFFRACTIONf_plane_restr0.003747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.379-2.48730.32931320.27632522X-RAY DIFFRACTION96
2.4873-2.61840.31731350.25822523X-RAY DIFFRACTION97
2.6184-2.78250.29981460.26032585X-RAY DIFFRACTION98
2.7825-2.99730.33981310.25122523X-RAY DIFFRACTION98
2.9973-3.29880.29081430.23892577X-RAY DIFFRACTION98
3.2988-3.7760.25971250.22152546X-RAY DIFFRACTION99
3.776-4.75670.24061410.19282580X-RAY DIFFRACTION99
4.7567-47.6670.24081300.20592564X-RAY DIFFRACTION98

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