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- PDB-7atv: Structure of protein kinase ck2 catalytic subunit (csnk2a2 gene p... -

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Basic information

Entry
Database: PDB / ID: 7atv
TitleStructure of protein kinase ck2 catalytic subunit (csnk2a2 gene product) in complex with the bivalent inhibitor KN2
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2 / bivalent inhibitor
Function / homology
Function and homology information


regulation of mitophagy / regulation of chromosome separation / Phosphorylation and nuclear translocation of the CRY:PER:kinase complex / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / Regulation of CDH1 posttranslational processing and trafficking to plasma membrane / protein kinase CK2 complex / : / Receptor Mediated Mitophagy / Synthesis of PC ...regulation of mitophagy / regulation of chromosome separation / Phosphorylation and nuclear translocation of the CRY:PER:kinase complex / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / Regulation of CDH1 posttranslational processing and trafficking to plasma membrane / protein kinase CK2 complex / : / Receptor Mediated Mitophagy / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins / negative regulation of apoptotic signaling pathway / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / liver regeneration / acrosomal vesicle / Signal transduction by L1 / cerebral cortex development / Wnt signaling pathway / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / chromatin / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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
Similarity search - Domain/homology
Chem-RXE / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.98 Å
AuthorsLindenblatt, D. / Applegate, V. / Nickelsen, A. / Klussmann, M. / Neundorf, I. / Goetz, C. / Jose, J. / Niefind, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/4-2 Germany
Citation
Journal: J.Med.Chem. / Year: 2022
Title: Molecular Plasticity of Crystalline CK2 alpha ' Leads to KN2, a Bivalent Inhibitor of Protein Kinase CK2 with Extraordinary Selectivity.
Authors: Lindenblatt, D. / Applegate, V. / Nickelsen, A. / Klussmann, M. / Neundorf, I. / Gotz, C. / Jose, J. / Niefind, K.
#1: Journal: ACS Omega / Year: 2019
Title: Diacritic Binding of an Indenoindole Inhibitor by CK2alpha Paralogs Explored by a Reliable Path to Atomic Resolution CK2alpha' Structures
Authors: Lindenblatt, D. / Nickelsen, A. / Applegate, V.M. / Hochscherf, J. / Witulski, B. / Bouaziz, Z. / Marminon, C. / Bretner, M. / Le Borgne, M. / Jose, J. / Niefind, K.
#2: Journal: J Med Chem / Year: 2020
Title: Structural and Mechanistic Basis of the Inhibitory Potency of Selected 2-Aminothiazole Compounds on Protein Kinase CK2.
Authors: Lindenblatt, D. / Nickelsen, A. / Applegate, V.M. / Jose, J. / Niefind, K.
History
DepositionOct 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Data collection / Database references / Category: citation / database_2 / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 9, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7544
Polymers42,8801
Non-polymers8743
Water7,999444
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-6 kcal/mol
Surface area15390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.783, 47.560, 50.998
Angle α, β, γ (deg.)66.804, 88.959, 88.745
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Casein kinase II subunit alpha' / CK II alpha'


Mass: 42879.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A2, CK2A2 / Production host: Escherichia coli (E. coli)
References: UniProt: P19784, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-RXE / ~{N}'-[2-(3,4-dichlorophenyl)ethyl]-~{N}-[4-[4,5,6,7-tetrakis(bromanyl)benzimidazol-1-yl]butyl]butanediamide / KN2


Mass: 776.968 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H22Br4Cl2N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Reservoir composition: 28 % (w/v) PEG6000, 0.9 M LiCl, 0.1 M, Tris/HCl, pH 8.5; drop composition prior to equilibration: 0.01 ml reservoir solution + 0.02 ml CK2alpha' (mutant Cys336Ser) ...Details: Reservoir composition: 28 % (w/v) PEG6000, 0.9 M LiCl, 0.1 M, Tris/HCl, pH 8.5; drop composition prior to equilibration: 0.01 ml reservoir solution + 0.02 ml CK2alpha' (mutant Cys336Ser) /inhibitor MB002 mixture (0.180 ml 6 mg/ml CK2alpha'Cys336Ser, 0.5 M NaCl, 25 mM Tris/HCl, pH 8.5, mixed and pre-equilibrated with 0.02 ml 10 mM MB002 in dimethyl sulfoxide); the initial inhibitor MB002 was replaced by the bivalent inhibitor KN2 by extensive crystal soaking.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.964→33.281 Å / Num. obs: 190713 / % possible obs: 78.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 10.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.03 / Rrim(I) all: 0.059 / Rsym value: 0.051 / Net I/σ(I): 12.4
Reflection shellResolution: 0.964→1.02 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.907 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 9537 / CC1/2: 0.514 / Rpim(I) all: 0.54 / Rrim(I) all: 1.057 / Rsym value: 0.907 / % possible all: 25.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874model building
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.98→33.28 Å / SU ML: 0.0624 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 14.3878
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1411 1931 1.02 %
Rwork0.1268 187904 -
obs0.127 189835 81.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.36 Å2
Refinement stepCycle: LAST / Resolution: 0.98→33.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 40 444 3252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01163198
X-RAY DIFFRACTIONf_angle_d1.17114349
X-RAY DIFFRACTIONf_chiral_restr0.0938433
X-RAY DIFFRACTIONf_plane_restr0.0093576
X-RAY DIFFRACTIONf_dihedral_angle_d20.99971249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.98-10.2726370.24683658X-RAY DIFFRACTION22.36
1-1.030.2369960.24349759X-RAY DIFFRACTION59.51
1.03-1.060.25251540.218312961X-RAY DIFFRACTION78.92
1.06-1.10.20291170.1813537X-RAY DIFFRACTION82.69
1.1-1.140.17591620.147214757X-RAY DIFFRACTION89.79
1.14-1.180.13611430.124914782X-RAY DIFFRACTION89.99
1.18-1.230.11421550.115614717X-RAY DIFFRACTION89.8
1.23-1.30.13411490.108114500X-RAY DIFFRACTION88.45
1.3-1.380.12531400.106913490X-RAY DIFFRACTION82.13
1.38-1.490.10161550.096415153X-RAY DIFFRACTION92.38
1.49-1.640.1211690.095915340X-RAY DIFFRACTION93.44
1.64-1.870.11931520.105815237X-RAY DIFFRACTION92.83
1.87-2.360.13481460.12514325X-RAY DIFFRACTION87.45
2.36-33.280.15211560.137215688X-RAY DIFFRACTION95.68

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