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- PDB-8qbu: STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALP... -

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Basic information

Entry
Database: PDB / ID: 8qbu
TitleSTRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 GENE PRODUCT) IN COMPLEX WITH THE INHIBITOR CX-4945 AND THE ALPHA-D-POCKET LIGAND 3,4-DICHLORO PHENETHYLAMINE (DPA)
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE / protein kinase CK2 casein kinase 2 inhibitor SGC-CK2-1
Function / homology
Function and homology information


regulation of mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Synthesis of PC / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...regulation of mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Synthesis of PC / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / 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 / Regulation of PTEN stability and activity / Wnt signaling pathway / 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-3NG / 2-(3,4-dichlorophenyl)ethanamine / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsWerner, C. / Niefind, K.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/11-1 Germany
German Research Foundation (DFG)NI 643/4-2 Germany
Citation
Journal: Kinases Phosphatases / Year: 2023
Title: Discovery and Exploration of Protein Kinase CK2 Binding Sites Using CK2alpha Cys336Ser as an Exquisite Crystallographic Tool
Authors: Werner, C. / Lindenblatt, D. / Viht, K. / Uri, A. / 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.
History
DepositionAug 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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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)44,16515
Polymers42,8801
Non-polymers1,28514
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint36 kcal/mol
Surface area15510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.173, 47.715, 50.586
Angle α, β, γ (deg.)66.050, 89.720, 88.970
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.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-42J / 2-(3,4-dichlorophenyl)ethanamine


Mass: 190.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9Cl2N / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-3NG / 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid


Mass: 349.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H12ClN3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: THE CK2ALPHA' SOLUTION AFTER PROTEIN PURIFICATION (5 MG/ML CK2ALPHA' IN 500 MM NACL, 25 MM TRIS/HCl, PH 8.5) WAS MIXED IN 1:10 VOLUME RATIO WITH 10 MM SOLUTION OF THE INHIBITOR MB002 IN DMSO. ...Details: THE CK2ALPHA' SOLUTION AFTER PROTEIN PURIFICATION (5 MG/ML CK2ALPHA' IN 500 MM NACL, 25 MM TRIS/HCl, PH 8.5) WAS MIXED IN 1:10 VOLUME RATIO WITH 10 MM SOLUTION OF THE INHIBITOR MB002 IN DMSO. THIS SOLUTION WAS MIXED IN 2:1 RATIO WITH RESERVOIR SOLUTION [900 MM LICL, 28 % (W/V) PEG 6000, 250 MM TRIS/HCL, PH 8.5] IN SITTING DROP PLATES (VAPOUR DIFFUSION). THE CRYSTAL GROWTH WAS INDUCED BY MICROSEEDING. THE CRYSTALS WERE OPTIMIZED BY MACROSEEDING. A CRYSTAL WAS PURGED TWICE WITH RESERVOIR SOLUTION BEFORE ADDING 1 MIKROLITER DPA (50 MM IN DMSO) AND 1 MIKROLITER CX-4945 (10 MM IN DMSO) TO THE CRYSTAL MOTHOR LIQUOR FOR EXTENSIVE SOAKING AND REPLACEMENT OF THE INITIAL INHIBITOR MB002. ALL STEPS WERE PERFORMED AT A TEMPERATURE OF 293 K.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.8566 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8566 Å / Relative weight: 1
ReflectionResolution: 1.09→46.17 Å / Num. obs: 118499 / % possible obs: 72.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 11.97 Å2 / CC1/2: 0.997 / Net I/σ(I): 6.5
Reflection shellResolution: 1.095→1.134 Å / Num. unique obs: 1763 / CC1/2: 0.608

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Processing

Software
NameVersionClassification
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.09→46.17 Å / SU ML: 0.0899 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.7104
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1793 1984 1.68 %
Rwork0.1593 116384 -
obs0.1596 118368 72.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.8 Å2
Refinement stepCycle: LAST / Resolution: 1.09→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 84 282 3130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01643060
X-RAY DIFFRACTIONf_angle_d1.41834131
X-RAY DIFFRACTIONf_chiral_restr0.1111419
X-RAY DIFFRACTIONf_plane_restr0.0163532
X-RAY DIFFRACTIONf_dihedral_angle_d13.17931191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.09-1.120.2522210.22891065X-RAY DIFFRACTION9.38
1.12-1.150.2424320.21641971X-RAY DIFFRACTION17.22
1.15-1.190.199520.22343548X-RAY DIFFRACTION31.05
1.19-1.220.22941040.22635149X-RAY DIFFRACTION45.15
1.22-1.270.2803980.2256768X-RAY DIFFRACTION59.16
1.27-1.320.22671410.20278658X-RAY DIFFRACTION75.6
1.32-1.380.2171740.196910131X-RAY DIFFRACTION89.02
1.38-1.450.20181810.185211043X-RAY DIFFRACTION96.41
1.45-1.540.20541980.16711261X-RAY DIFFRACTION98.56
1.54-1.660.17961860.157911276X-RAY DIFFRACTION98.94
1.66-1.830.16952000.145811313X-RAY DIFFRACTION99.17
1.83-2.090.14961950.134711377X-RAY DIFFRACTION99.57
2.09-2.640.14521980.149311421X-RAY DIFFRACTION99.94
2.64-46.170.18722040.156511403X-RAY DIFFRACTION99.94

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