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- PDB-9gxy: Crystal structure of protein kinase CK2 catalytic subunit (CSNK2A... -

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Basic information

Entry
Database: PDB / ID: 9gxy
TitleCrystal structure of protein kinase CK2 catalytic subunit (CSNK2A2 gene product) in complex with the dual CK2/HDAC inhibitor IOR-160
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2 / dual CK2/HDAC inhibitor
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 / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins ...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 / 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 / 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
: / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsWerner, C. / Lindenblatt, D. / Niefind, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/11-1 Germany
CitationJournal: Acs Pharmacol Transl Sci / Year: 2025
Title: Targeting Casein Kinase 2 and Histone Deacetylase with a Dual Inhibitor Effectively Reduces Tumor Growth in a Triple-Negative Breast Cancer Xenograft Model.
Authors: Ortin, I. / Ochoa-Callejero, L. / Werner, C. / Lindenblatt, D. / Niefind, K. / Martinez, A. / de Pascual-Teresa, B. / Ramos, A.
History
DepositionOct 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: 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)43,2762
Polymers42,8801
Non-polymers3961
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.343, 47.734, 50.706
Angle α, β, γ (deg.)66.580, 89.780, 88.990
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 / Mutation: C336S
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-A1IKB / 5-[[8-(oxidanylamino)-8-oxidanylidene-octyl]amino]benzo[c][2,6]naphthyridine-8-carboxylic acid / 5-[[8-(hydroxyamino)-8-oxooctyl]amino]benzo[c][2,6]naphthyridine-8-carboxylic acid


Mass: 396.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Original crystal: 47.5 microliter CK2alphaPrime mixed with 2.5 microliter of a 20 mM CX-4945 solution in DMSO to a final concentration of 5 mg per mL protein and 1 mM CX-4945. Reservoir (900 ...Details: Original crystal: 47.5 microliter CK2alphaPrime mixed with 2.5 microliter of a 20 mM CX-4945 solution in DMSO to a final concentration of 5 mg per mL protein and 1 mM CX-4945. Reservoir (900 mM LiCl, 250 mM TRIS HCl, pH 8.5, 28 % PEG 6000) was mixed 1:2 with protein stock. Crystal were optimized by micro- and macroseeding. IOR-160 was introduced by back-soaking: 8 microliter reservoir were mixed for this with with 2 microliter of a 10 mM IOR-160 stock in DMSO. The crystal was soaked in 4 microliters of this solution of 72 hours.

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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: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.157→46.529 Å / Num. obs: 84256 / % possible obs: 59.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 9.5 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.028 / Rrim(I) all: 0.078 / Net I/σ(I): 16
Reflection shellResolution: 1.161→1.202 Å / Rmerge(I) obs: 2.182 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 426 / CC1/2: 0.694

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.16→41.06 Å / SU ML: 0.0795 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.3119
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1778 1980 2.35 %
Rwork0.1602 82133 -
obs0.1606 84113 60.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.33 Å2
Refinement stepCycle: LAST / Resolution: 1.16→41.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 29 359 3147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123017
X-RAY DIFFRACTIONf_angle_d1.27394093
X-RAY DIFFRACTIONf_chiral_restr0.1102417
X-RAY DIFFRACTIONf_plane_restr0.0137530
X-RAY DIFFRACTIONf_dihedral_angle_d13.99041162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.16-1.190.297730.2043128X-RAY DIFFRACTION1.32
1.19-1.220.2535130.2311740X-RAY DIFFRACTION7.58
1.22-1.250.2451390.22781608X-RAY DIFFRACTION16.56
1.25-1.290.2459610.22822512X-RAY DIFFRACTION25.95
1.29-1.340.266950.21373983X-RAY DIFFRACTION40.98
1.34-1.390.22981180.20275311X-RAY DIFFRACTION54.6
1.39-1.460.22182260.18358404X-RAY DIFFRACTION86.47
1.46-1.530.24211820.17378317X-RAY DIFFRACTION85.59
1.53-1.630.17982220.16768627X-RAY DIFFRACTION89.02
1.63-1.760.16722000.16278308X-RAY DIFFRACTION85.3
1.76-1.930.17852150.16048710X-RAY DIFFRACTION89.71
1.93-2.210.15422050.15558333X-RAY DIFFRACTION85.73
2.21-2.790.18441940.15878368X-RAY DIFFRACTION86.28
2.79-41.060.15512070.14338784X-RAY DIFFRACTION90.22
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.647275057936-0.352493590597-0.1870860774361.617152448480.3652675128460.508262072696-0.0517840141551-0.00692322902414-0.0602607019192-0.0012327235380.02585895468250.112068659860.1058257332190.008028973487840.03670469267720.0736164129599-0.00554798550078-0.01659873796730.0642007219890.0123763596630.0630916029822-5.62115159974-14.7073105207-10.494614253
21.123859737040.135406686028-0.0900406771130.872049431216-0.1335472449140.754158354356-0.00472497878792-0.09557349233130.04273711550770.0342000064606-0.00570468250977-0.0221814579769-0.0243823058660.07951457923380.007420955628550.04344224820810.00649307220626-0.005389946977350.0532482557737-0.00592260526140.04240355056056.839913519153.20805291731-2.96191460175
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 130 )7 - 1301 - 124
22chain 'A' and (resid 131 through 333 )131 - 333125 - 327

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