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- PDB-9h97: Structure of protein kinase CK2 catalytic subunit CK2alpha (CSNK2... -

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Basic information

Entry
Database: PDB / ID: 9h97
TitleStructure of protein kinase CK2 catalytic subunit CK2alpha (CSNK2A1 gene product) in complex with the indenoindole-type inhibitor MC11 at high-salt conditions
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / Protein kinase / CK2 / casein kinase II / indenoindole
Function / homology
Function and homology information


regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of signal transduction by p53 class mediator / Maturation of hRSV A proteins / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / : / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / PML body / Regulation of PTEN stability and activity / Wnt signaling pathway / positive regulation of protein catabolic process / kinase activity / KEAP1-NFE2L2 pathway / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / DNA damage response / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / 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: 1.7 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)42,2802
Polymers41,6851
Non-polymers5951
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15380 Å2
Unit cell
Length a, b, c (Å)72.582, 72.582, 133.053
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-683-

HOH

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Components

#1: Protein Casein kinase II subunit alpha


Mass: 41685.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P68400
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.1 Å3/Da / Density % sol: 41.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Reservoir: 4.2 M NaCl, 0.1 M sodium citrat pH 8.5 Protein 5 mg per mL including 1 mM MC11 in DMSO Drop: Mixing 1 microliter protein incl. MC11 with 1 microliter reservoir solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.7→49.04 Å / Num. obs: 39909 / % possible obs: 99.9 % / Redundancy: 12.4 % / Biso Wilson estimate: 31.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.017 / Rrim(I) all: 0.061 / Net I/σ(I): 21.2
Reflection shellResolution: 1.7→1.761 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2037 / CC1/2: 0.672 / Rpim(I) all: 0.553 / Rrim(I) all: 1.26 / Rsym value: 1.128

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→49.04 Å / SU ML: 0.2086 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8487
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2309 2000 5.01 %
Rwork0.1968 37909 -
obs0.1985 39909 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.32 Å2
Refinement stepCycle: LAST / Resolution: 1.7→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 25 183 3020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722915
X-RAY DIFFRACTIONf_angle_d0.87573948
X-RAY DIFFRACTIONf_chiral_restr0.0571405
X-RAY DIFFRACTIONf_plane_restr0.0108506
X-RAY DIFFRACTIONf_dihedral_angle_d13.91031100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.37851390.31072649X-RAY DIFFRACTION99.93
1.74-1.790.3051410.25212657X-RAY DIFFRACTION100
1.79-1.840.25061400.22552663X-RAY DIFFRACTION100
1.84-1.90.26031400.22122665X-RAY DIFFRACTION99.96
1.9-1.970.25321420.22432664X-RAY DIFFRACTION100
1.97-2.050.24711410.2042672X-RAY DIFFRACTION100
2.05-2.140.25181420.19382691X-RAY DIFFRACTION100
2.14-2.250.23661400.19612666X-RAY DIFFRACTION100
2.25-2.40.23471430.19552691X-RAY DIFFRACTION99.96
2.4-2.580.2561420.2142712X-RAY DIFFRACTION100
2.58-2.840.25291440.22472713X-RAY DIFFRACTION100
2.84-3.250.27171440.22312738X-RAY DIFFRACTION100
3.25-4.10.19041480.17292793X-RAY DIFFRACTION100
4.1-49.040.20871540.17522935X-RAY DIFFRACTION99.9
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)
11.4419033383-0.3881198637520.7346850830932.23216071505-1.169741354813.89491497859-0.0890454539534-0.1642604223090.004404516243080.009064032935180.113544887080.291909705685-0.571102573282-0.40897613510.003703624512710.3000944735730.0406756666420.007994117510920.332981318034-0.01925321463020.28717777813-23.11641355692.5128655233630.3298520775
22.25091668791-0.528168600102-0.06658947295571.740242380660.9138044899832.362959517830.07882457622190.286515170346-0.00980236477394-0.240273370668-0.05146295136690.0110828094805-0.179660209470.1573479123130.01416632454620.1486650515950.0089710067705-0.005100805638750.2449779071790.02463360460410.202167378352-13.0795255425-10.462056507421.6183781567
32.94424017594-0.487511148012-0.2069189857582.02127826780.5411666544063.08252376324-0.01417666803770.319225313796-0.675293050677-0.06536919264640.231133802962-0.1272911349280.4664557766540.4904040211110.109344227660.2684671061120.112996317042-0.03145262608750.428828012669-0.03921217559980.405007932993-5.32265266237-22.4038594221.6742990645
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 2 through 108 )2 - 1081 - 107
22chain 'A' and (resid 109 through 249 )109 - 249108 - 248
33chain 'A' and (resid 250 through 334 )250 - 334249 - 333

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