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- PDB-9hk5: Structure of a mutant of human protein kinase CK2alpha' that equa... -

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Basic information

Entry
Database: PDB / ID: 9hk5
TitleStructure of a mutant of human protein kinase CK2alpha' that equals its isoenzyme CK2alpha in affinity to the regulatory subunit CK2beta
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE / human protein kinase CK2 human casein kinase 2 isoenzymes CK2alpha and CK2alpha' CK2alpha/CK2beta interaction
Function / homology
Function and homology information


regulation of mitophagy / regulation of chromosome separation / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / 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 / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / 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 / acrosomal vesicle / liver regeneration / 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 / 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 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 / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.491 Å
AuthorsWerner, C. / Niefind, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/11-1 Germany
Citation
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.
#1: Journal: J Mol Biol / Year: 2011
Title: Structure of the human protein kinase CK2 catalytic subunit CK2alpha' and interaction thermodynamics with the regulatory subunit CK2beta
Authors: Bischoff, N. / Olsen, B. / Raaf, J. / Bretner, M. / Issinger, O.G. / Niefind, K.
History
DepositionDec 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,3824
Polymers42,9081
Non-polymers4743
Water6,071337
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint3 kcal/mol
Surface area15730 Å2
Unit cell
Length a, b, c (Å)46.788, 47.804, 50.579
Angle α, β, γ (deg.)111.757, 90.221, 91.546
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: 42907.965 Da / Num. of mol.: 1 / Mutation: P32V, V83I, T101I, 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: 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 / Comment: chemotherapy, inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: protein stock solution: 5 mg/ml protein, 500 mM NaCl, 25 mM Tris/HCl, pH 8.5; protein/inhibitor mixture: 19 mikroliter protein stock solution plus 1 mikroliter 20 mM CX-4945 in DMSO; ...Details: protein stock solution: 5 mg/ml protein, 500 mM NaCl, 25 mM Tris/HCl, pH 8.5; protein/inhibitor mixture: 19 mikroliter protein stock solution plus 1 mikroliter 20 mM CX-4945 in DMSO; reservoir: 900 mM LiCL, 28 % (w/v) PEG 6000, 250 mM Tris/HCl, pH 8.5; crystallization drop: 2 mikroliter reservoir + 4 mikroliter protein/inhibitor mixture; initial crystals were optimized by micro seeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.873128 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 1.491→46.971 Å / Num. obs: 44234 / % possible obs: 88.3 % / Redundancy: 2.8 % / Biso Wilson estimate: 9.63 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.076 / Rrim(I) all: 0.129 / Rsym value: 0.104 / Net I/σ(I): 7.7
Reflection shellResolution: 1.491→1.672 Å / Redundancy: 3 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2189 / CC1/2: 0.447 / Rpim(I) all: 0.533 / Rrim(I) all: 0.944 / Rsym value: 0.775 / % possible all: 11.4

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Processing

Software
NameVersionClassification
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
PHENIX1.21_5207refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.491→46.97 Å / SU ML: 0.1324 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.1756
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2038 1091 2.47 %
Rwork0.1741 43143 -
obs0.1748 44234 66.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.8 Å2
Refinement stepCycle: LAST / Resolution: 1.491→46.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2770 0 33 337 3140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632909
X-RAY DIFFRACTIONf_angle_d0.79353928
X-RAY DIFFRACTIONf_chiral_restr0.0856403
X-RAY DIFFRACTIONf_plane_restr0.0077502
X-RAY DIFFRACTIONf_dihedral_angle_d13.31861102
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.491-1.560.389230.2077100X-RAY DIFFRACTION1.25
1.56-1.640.2515260.24531159X-RAY DIFFRACTION14.33
1.64-1.740.2821030.24873873X-RAY DIFFRACTION47.92
1.74-1.880.2441710.22416477X-RAY DIFFRACTION80.26
1.88-2.070.23751950.19917648X-RAY DIFFRACTION95.11
2.07-2.370.21132000.17467936X-RAY DIFFRACTION97.69
2.37-2.980.21930.17147964X-RAY DIFFRACTION98.38
2.98-46.970.1642000.14197986X-RAY DIFFRACTION98.83
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)
10.1156487120120.0897952463832-0.05611741302980.0690140956982-0.03127461257170.171858161667-0.02790338485470.0205905244722-0.0736260239821-0.02820028626620.0421554316690.04726701612580.0376358593816-0.01386624380930.006773612330690.0719121683975-0.001684321417690.007259329276910.0715708453580.0009343314688720.12844262180162.909119001441.556873470.232137754921
20.6386408683020.167917967768-0.3707462474750.623782973398-0.5044527844240.51745319991-0.00827248949820.0821905928730.0544300486203-0.00301079196910.0857560510990.07529035344030.117183927427-0.06514297501280.08279401741460.0967492670151-0.000692094590455-0.007200336882690.04661846109760.002547903100960.048821412450450.32641923625.09579237168.54775330715
30.452163829225-0.233151056453-0.1009440968420.4103016285460.05894815996030.308970499856-0.0391655930130.00507596926413-0.08346485365190.0807904389760.01772787425150.05100812574470.12487789881-0.0355040860887-0.01641630075430.04669071828120.000523061879707-0.007634683346340.0300266040905-0.005238572107930.046065760452245.543479905938.427366475911.7591751835
40.261317056849-0.06638715962770.1160446532730.2012051911590.01066053638790.143042068109-0.01591363972550.0158473634403-0.0267891942988-0.003562981316060.007121978675450.0132633360850.02701529615240.00545537580182-0.1875824890760.032999460541-0.006787970350190.001582839412990.03549366990420.00453230872010.030426118000544.821820827343.51648939290.351796585968
50.452915606867-0.0129349947508-0.2508927174990.4727854426740.04778023690140.2273948561150.07589352591840.3299533460450.0928569915756-0.227644744218-0.05526166262670.180507952416-0.0720317820191-0.267933623137-0.287600083910.00287022297186-0.00735645398088-0.004993013017040.08420617631380.0287316804172-0.0027876603620432.252408944353.2380409648-7.23382168403
60.3019616711070.0840816858529-0.01008698516560.5170859052810.03493654223070.158739007730.0526527569467-0.001129318078590.1347693103150.1301783131620.0134489236898-0.141442770577-0.0841381552630.01171827211830.02465123001140.0628779906839-0.0186573150597-0.0007311553491810.00760838894145-0.004453209492450.048130556852943.685647365957.73046709588.26535397727
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 36 )7 - 361 - 30
22chain 'A' and (resid 37 through 88 )37 - 8831 - 82
33chain 'A' and (resid 89 through 150 )89 - 15083 - 144
44chain 'A' and (resid 151 through 228 )151 - 228145 - 222
55chain 'A' and (resid 229 through 305 )229 - 305223 - 299
66chain 'A' and (resid 306 through 334 )306 - 334300 - 328

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