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- PDB-9i12: Human protein kinase CK2 alpha in complex with TN17 -

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Basic information

Entry
Database: PDB / ID: 9i12
TitleHuman protein kinase CK2 alpha in complex with TN17
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: 2 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)39,9485
Polymers39,3041
Non-polymers6454
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-47 kcal/mol
Surface area15700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.077, 45.855, 62.606
Angle α, β, γ (deg.)90.00, 111.23, 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-A1IYX / (2~{Z},5~{Z})-5-[(4-methoxy-3-oxidanyl-phenyl)methylidene]-2-(4-methoxyphenyl)imino-1,3-thiazolidin-4-one


Mass: 356.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16N2O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 1.98 Å3/Da / Density % sol: 37.79 %
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: 2→58.36 Å / Num. obs: 20975 / % possible obs: 99.9 % / Redundancy: 5.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.04 / Rrim(I) all: 0.097 / Χ2: 0.97 / Net I/σ(I): 11.7 / Num. measured all: 122464
Reflection shellResolution: 2→2.05 Å / % possible obs: 100 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.879 / Num. measured all: 8943 / Num. unique obs: 1516 / CC1/2: 0.746 / Rpim(I) all: 0.388 / Rrim(I) all: 0.963 / Χ2: 1.01 / Net I/σ(I) obs: 2.3

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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: 2→49.653 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2233 992 4.73 %
Rwork0.1658 --
obs0.1684 20952 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→49.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 40 136 2949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072927
X-RAY DIFFRACTIONf_angle_d0.8643969
X-RAY DIFFRACTIONf_dihedral_angle_d15.6641751
X-RAY DIFFRACTIONf_chiral_restr0.054407
X-RAY DIFFRACTIONf_plane_restr0.005508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.10550.27151390.21232804X-RAY DIFFRACTION100
2.1055-2.23740.2751410.19462827X-RAY DIFFRACTION100
2.2374-2.41020.26791650.18522823X-RAY DIFFRACTION100
2.4102-2.65270.26531500.17842841X-RAY DIFFRACTION100
2.6527-3.03650.22931270.17182842X-RAY DIFFRACTION100
3.0365-3.82550.21061320.15442890X-RAY DIFFRACTION100
3.8255-49.6530.1881380.15132933X-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)
13.54080.7448-1.35482.2074-0.99113.8076-0.36170.1756-0.5961-0.31570.0115-0.18480.73020.25650.36110.44770.08570.03020.2637-0.03940.38123.1839-32.3387-48.1663
20.29890.9731-0.01823.61120.31291.824-0.12060.3293-0.5475-0.02230.4263-0.47670.28681.036-0.12450.34220.2329-0.08270.6345-0.14010.579827.4472-16.6587-47.0703
32.86891.50341.06782.4761.2540.91170.06060.2233-0.13190.1650.063-0.21630.16740.598-0.09270.24510.0791-0.00020.5269-0.04960.267821.4782-14.0268-46.043
43.00510.30581.17650.6605-0.3560.7936-0.18280.03280.19940.37630.1899-0.0703-0.32250.32220.02010.3998-0.0172-0.01940.4278-0.08310.350214.942-4.0152-45.3415
51.698-0.0998-0.5740.8961-0.08752.1425-0.0177-0.06270.05560.11260.0667-0.00780.06790.1645-0.04520.21250.0089-0.01990.1934-0.01580.2145-1.819-14.4674-39.23
61.5504-0.38210.14783.0066-0.35712.450.0010.1380.0753-0.07010.11670.0874-0.1108-0.1703-0.14040.1847-0.0079-0.00650.18610.01520.2464-10.4361-8.9365-48.6257
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 44 )
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 103 )
4X-RAY DIFFRACTION4chain 'A' and (resid 104 through 129 )
5X-RAY DIFFRACTION5chain 'A' and (resid 130 through 280 )
6X-RAY DIFFRACTION6chain 'A' and (resid 281 through 330 )

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