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- PDB-9h96: STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALP... -

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Basic information

Entry
Database: PDB / ID: 9h96
TitleSTRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 GENE PRODUCT) IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR MC11
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE / ATP-competitive inhibitor / kinase / CK2 / Casein Kinase II
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 / 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
: / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsNiefind, K. / Lindenblatt, D. / Werner, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/11-1 Germany
Citation
Journal: Biol.Chem. / Year: 2025
Title: Exploring the biological potential of the brominated indenoindole MC11 and its interaction with protein kinase CK2.
Authors: Marminon, C. / Werner, C. / Gast, A. / Herfindal, L. / Charles, J. / Lindenblatt, D. / Aichele, D. / Mularoni, A. / Doskeland, S.O. / Jose, J. / Niefind, K. / Le Borgne, M.
#1: Journal: Biol.Chem. / Year: 2025
Title: Exploring the biological potential of the brominated indenoindole MC11 and its interaction with protein kinase CK2
Authors: Marminon, C. / Werner, C. / Gast, A. / Herfindal, L. / Charles, J. / Lindenblatt, D. / Aichele, D. / Mularoni, A. / Doskeland, S.O. / Jose, J. / Niefind, K. / Le Borgne, M.
History
DepositionOct 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation / citation_author

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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)43,6085
Polymers42,8801
Non-polymers7284
Water8,233457
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-15 kcal/mol
Surface area14820 Å2
Unit cell
Length a, b, c (Å)46.294, 47.709, 50.359
Angle α, β, γ (deg.)66.370, 89.780, 89.090
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-A1ITG / 1,2,3,4-tetrakis(bromanyl)-5-propan-2-yl-7,8-dihydro-6~{H}-indeno[1,2-b]indole-9,10-dione


Mass: 594.917 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H13Br4NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 28 % (w/v) PEG 6000, 100 mM TRIS-HCl pH 8.5, 900 mM LiCl and 1 mM MB002, Growth and optimization by micro- and macroseeding. MC11 was introduced by backsoaking in a solution containing 2 mM MC11

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873127 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873127 Å / Relative weight: 1
ReflectionResolution: 1.04→46.29 Å / Num. obs: 138075 / % possible obs: 73.6 % / Redundancy: 12.4 % / Biso Wilson estimate: 11.29 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.04 / Rrim(I) all: 0.144 / Net I/σ(I): 9.2
Reflection shellResolution: 1.04→1.081 Å / Rmerge(I) obs: 2.292 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6904 / CC1/2: 0.492 / Rpim(I) all: 0.736 / Rrim(I) all: 2.413

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.04→46.29 Å / SU ML: 0.0965 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.0754
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1856 7212 5.23 %
Rwork0.172 130785 -
obs0.1727 137997 73.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.33 Å2
Refinement stepCycle: LAST / Resolution: 1.04→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 31 457 3247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01752941
X-RAY DIFFRACTIONf_angle_d1.52473987
X-RAY DIFFRACTIONf_chiral_restr0.1108407
X-RAY DIFFRACTIONf_plane_restr0.0168512
X-RAY DIFFRACTIONf_dihedral_angle_d13.88971120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.04-1.060.692210.28129X-RAY DIFFRACTION2.08
1.06-1.070.1949170.33226X-RAY DIFFRACTION3.92
1.07-1.080.2975240.3063460X-RAY DIFFRACTION7.78
1.08-1.090.3008390.3011721X-RAY DIFFRACTION12.17
1.09-1.110.3258770.28751045X-RAY DIFFRACTION17.91
1.11-1.120.3075720.2871411X-RAY DIFFRACTION23.69
1.12-1.140.30641020.27522026X-RAY DIFFRACTION33.97
1.14-1.160.27711110.27432554X-RAY DIFFRACTION42.67
1.16-1.180.28791700.26383029X-RAY DIFFRACTION51.44
1.18-1.190.25361820.25863665X-RAY DIFFRACTION61.07
1.19-1.220.26032230.25094428X-RAY DIFFRACTION74.69
1.22-1.240.262650.24635454X-RAY DIFFRACTION91.5
1.24-1.260.2433320.23675761X-RAY DIFFRACTION97.12
1.26-1.290.23143420.22065815X-RAY DIFFRACTION98.01
1.29-1.320.20133630.21265730X-RAY DIFFRACTION98.29
1.32-1.350.23313440.19495821X-RAY DIFFRACTION98.48
1.35-1.380.20443550.19045806X-RAY DIFFRACTION98.53
1.38-1.420.19533320.17735821X-RAY DIFFRACTION98.78
1.42-1.460.20673340.17235891X-RAY DIFFRACTION98.92
1.46-1.510.16873340.1695808X-RAY DIFFRACTION99.02
1.51-1.560.17522980.16235944X-RAY DIFFRACTION99.19
1.56-1.620.16893320.1595900X-RAY DIFFRACTION99.33
1.62-1.70.17062790.16195931X-RAY DIFFRACTION99.44
1.7-1.780.17934060.16735850X-RAY DIFFRACTION99.55
1.78-1.90.20523500.16625843X-RAY DIFFRACTION99.66
1.9-2.040.1772900.16165938X-RAY DIFFRACTION99.76
2.04-2.250.19332950.15995948X-RAY DIFFRACTION99.79
2.25-2.570.1772940.16365985X-RAY DIFFRACTION99.97
2.57-3.240.19082960.16685941X-RAY DIFFRACTION99.97
3.24-46.290.14843530.14845904X-RAY DIFFRACTION99.95
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)
10.298718176355-0.238241959639-0.08338476832410.6553682116020.1367638249990.197013917267-0.0361920672276-0.0231633695327-0.0177658774151-0.007455556074070.03419474219980.09492678822920.0778577301497-0.001344737209654.4626550724E-50.113077934495-0.00606623312752-0.006925771761390.1012349474420.005739630978510.11395553589-5.23872869519-14.7395698293-10.8945428625
20.6794063600310.0354017342976-0.01527672027890.573407145167-0.123953696080.6063092842060.00713747314788-0.05210284827420.0220787506021-0.00490283140679-0.00459153008632-0.0120194580036-0.01651209162150.0476585310888-6.73883863246E-50.03974429653890.003613013290080.00201186633810.0485893054153-0.003278427134380.0429397321716.897444631253.26390780268-3.80600984582
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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