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- PDB-9i13: Human protein kinase CK2 alpha in complex with TN19 -

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Basic information

Entry
Database: PDB / ID: 9i13
TitleHuman protein kinase CK2 alpha in complex with TN19
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / kinase domain
Function / homology
Function and homology information


regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Maturation of hRSV A proteins / Sin3-type complex ...regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Maturation of hRSV A proteins / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / 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 / Wnt signaling pathway / Regulation of PTEN stability and activity / 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 / 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 / regulation of cell cycle / negative regulation of translation / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / 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: 1.75 Å
AuthorsDalle Vedove, A. / Cazzanelli, G. / Lolli, G.
Funding support1items
OrganizationGrant numberCountry
Other governmentPoC Road to Market 2023
CitationJournal: To Be Published
Title: Switching off CK2-mediated activation of survivin offers new therapeutic opportunities in neuroblastoma
Authors: Cazzanelli, G. / Dalle Vedove, A. / Broso, F. / Burigotto, M. / Zasso, J. / Aiello, G. / Zonta, F. / Astolfi, A. / Barreca, M.L. / Ruzzene, M. / Tiberi, L. / Fava, L.L. / Quattrone, A. / Lolli, G.
History
DepositionJan 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 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)39,9986
Polymers39,3041
Non-polymers6955
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-43 kcal/mol
Surface area15540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.491, 46.613, 63.412
Angle α, β, γ (deg.)90.00, 111.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 39303.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-A1IYY / (2~{Z},5~{Z})-2-(3-fluorophenyl)imino-5-[(4-methoxy-3-oxidanyl-phenyl)methylidene]-1,3-thiazolidin-4-one


Mass: 344.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13FN2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.04 Å3/Da / Density % sol: 39.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 32% PEG4000, 0.2 M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→58.9 Å / Num. obs: 31952 / % possible obs: 99.1 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.021 / Rrim(I) all: 0.053 / Χ2: 0.94 / Net I/σ(I): 19.5 / Num. measured all: 195348
Reflection shellResolution: 1.75→1.78 Å / % possible obs: 86.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.563 / Num. measured all: 6950 / Num. unique obs: 1520 / CC1/2: 0.777 / Rpim(I) all: 0.29 / Rrim(I) all: 0.638 / Χ2: 0.94 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→36.551 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1945 1529 4.79 %
Rwork0.1603 --
obs0.162 31926 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→36.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 43 234 3050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062914
X-RAY DIFFRACTIONf_angle_d0.8553948
X-RAY DIFFRACTIONf_dihedral_angle_d16.3811734
X-RAY DIFFRACTIONf_chiral_restr0.056405
X-RAY DIFFRACTIONf_plane_restr0.005504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80650.25271420.21462515X-RAY DIFFRACTION91
1.8065-1.87110.21841430.18552758X-RAY DIFFRACTION100
1.8711-1.9460.24091320.17372758X-RAY DIFFRACTION100
1.946-2.03450.24351210.17292790X-RAY DIFFRACTION100
2.0345-2.14180.17811380.16672749X-RAY DIFFRACTION99
2.1418-2.2760.23371290.17032796X-RAY DIFFRACTION100
2.276-2.45170.20161550.17132794X-RAY DIFFRACTION100
2.4517-2.69830.22561450.17522752X-RAY DIFFRACTION100
2.6983-3.08860.22551310.17352815X-RAY DIFFRACTION100
3.0886-3.89060.16941520.14532804X-RAY DIFFRACTION100
3.8906-36.5510.16221410.14282866X-RAY DIFFRACTION100
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)
10.2240.0393-0.060.0356-0.02980.7116-0.09870.0621-0.20250.01140.0854-0.18750.15470.068400.22140.03750.01190.1926-0.07610.318515.4547-24.6896-48.0628
20.58390.377-0.11550.18950.13610.58860.02150.0734-0.02980.0085-0.0056-0.0781-0.04070.1312-0.00010.1713-0.0033-0.02290.226-0.0250.246319.9547-10.8669-45.7466
31.0051-0.0533-0.55030.4535-0.00980.7249-0.00690.1271-0.00080.05460.0334-0.0531-0.0021-0.11300.16870.0123-0.00970.1568-0.00580.1469-3.7243-13.0194-41.799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 330 )

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