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- PDB-9fbi: Structure of human protein kinase CK2 catalytic subunit (CK2alpha... -

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Basic information

Entry
Database: PDB / ID: 9fbi
TitleStructure of human protein kinase CK2 catalytic subunit (CK2alpha', CSNK2A2 gene product) in complex with the cyclic peptidomimetic compound 12 discovered by high-throughput screening
Components
  • Casein kinase II subunit alpha'
  • Cyclic peptidomimetic compound FMP37
KeywordsTRANSFERASE / human protein kinase ck2 catalytic subunit alpha' / csnk2a2 gene product / inhibition of ck2alpha/ck2beta subunit interaction
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
NICOTINIC ACID / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.161 Å
AuthorsNiefind, K. / Werner, C. / Pietsch, M. / Eimermacher, S. / Lindenblatt, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/11-1 Germany
Citation
Journal: To Be Published
Title: Discovery and characterization of a novel class of cyclic peptidic compounds inhibiting the assembly of the protein kinase CK2alpha2/beta2 holoenzyme
Authors: Werner, C. / Eimermacher, S. / Lindenblatt, D. / Niefind, K. / Pietsch, M.
#1: Journal: Biol.Chem. / Year: 2025
Title: A CK2 alpha ' mutant indicating why CK2 alpha and CK2 alpha ', the isoforms of the catalytic subunit of human protein kinase CK2, deviate in affinity to CK2 beta.
Authors: Werner, C. / Eimermacher, S. / Harasimowicz, H. / Fischer, D. / Pietsch, M. / Niefind, K.
#2: Journal: ACS Chem Biol / Year: 2013
Title: First structure of protein kinase CK2 catalytic subunit with an effective CK2beta-competitive ligand.
Authors: Raaf, J. / Guerra, B. / Neundorf, I. / Bopp, B. / Issinger, O.G. / Jose, J. / Pietsch, M. / Niefind, K.
History
DepositionMay 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Casein kinase II subunit alpha'
B: Casein kinase II subunit alpha'
E: Cyclic peptidomimetic compound FMP37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,54119
Polymers86,4913
Non-polymers1,04916
Water8,449469
1
A: Casein kinase II subunit alpha'
E: Cyclic peptidomimetic compound FMP37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,14210
Polymers43,6112
Non-polymers5318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3989
Polymers42,8801
Non-polymers5198
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.452, 71.068, 102.878
Angle α, β, γ (deg.)90.000, 91.967, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABE

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


Mass: 42879.867 Da / Num. of mol.: 2
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: Protein/peptide Cyclic peptidomimetic compound FMP37


Mass: 731.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)

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Non-polymers , 5 types, 485 molecules

#3: Chemical ChemComp-NIO / NICOTINIC ACID


Mass: 123.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: protein solution: 90 mikroliter CK2alpha'-Cys336Ser solution (5 mg/ml in 500 mmol/l NaCl, 25 mmol/l Tris/HCl, pH 8.5) was mixed with 10 mikroliter 10 millimolar FMP37 in DMSO and incubated ...Details: protein solution: 90 mikroliter CK2alpha'-Cys336Ser solution (5 mg/ml in 500 mmol/l NaCl, 25 mmol/l Tris/HCl, pH 8.5) was mixed with 10 mikroliter 10 millimolar FMP37 in DMSO and incubated for 30 min. reservoir: 810 mmol/l LiCl, 100 mM Tris/HCl, pH 8.5, 28%(w/v) PEG6000. crystallization drop: 4 mikroliter protein solution plus 2 mikroliter reservoir solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.885602 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885602 Å / Relative weight: 1
ReflectionResolution: 1.161→58.462 Å / Num. obs: 119426 / % possible obs: 52 % / Redundancy: 4.9 % / Biso Wilson estimate: 13.04 Å2 / CC1/2: 0.906 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.04 / Rrim(I) all: 0.096 / Rsym value: 0.081 / Net I/σ(I): 7.2
Reflection shellResolution: 1.161→1.329 Å / Rmerge(I) obs: 1.275 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5971 / CC1/2: 0.535 / Rpim(I) all: 0.77 / Rrim(I) all: 1.436 / Rsym value: 1.275

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.161→58.46 Å / SU ML: 0.1206 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.4113
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1847 1205 1.01 %
Rwork0.1452 118163 -
obs0.1456 119368 51.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.49 Å2
Refinement stepCycle: LAST / Resolution: 1.161→58.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5528 0 117 469 6114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01815896
X-RAY DIFFRACTIONf_angle_d1.42797953
X-RAY DIFFRACTIONf_chiral_restr0.1042817
X-RAY DIFFRACTIONf_plane_restr0.01511022
X-RAY DIFFRACTIONf_dihedral_angle_d14.84042244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.161-1.210.202360.2403512X-RAY DIFFRACTION2.04
1.21-1.260.3281170.24991658X-RAY DIFFRACTION6.59
1.26-1.330.2469380.22923726X-RAY DIFFRACTION14.75
1.33-1.410.2477770.21276890X-RAY DIFFRACTION27.39
1.41-1.520.23611310.194712233X-RAY DIFFRACTION48.58
1.52-1.670.22472390.172223536X-RAY DIFFRACTION93.19
1.67-1.920.18242190.150922313X-RAY DIFFRACTION88.12
1.92-2.420.17722280.137923011X-RAY DIFFRACTION90.84
2.42-58.460.17272500.133724284X-RAY DIFFRACTION94.76

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