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- PDB-9i17: Human protein kinase CK2 alpha in complex with TN20 -

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Basic information

Entry
Database: PDB / ID: 9i17
TitleHuman protein kinase CK2 alpha in complex with TN20
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / kinase domain
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 / Maturation of hRSV A proteins ...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 / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of signal transduction by p53 class mediator / 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: 1.55 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 16, 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)40,1117
Polymers39,3041
Non-polymers8076
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-56 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.402, 46.506, 63.315
Angle α, β, γ (deg.)90.00, 111.50, 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.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-A1IYZ / (2~{Z},5~{Z})-2-(3-chlorophenyl)imino-5-[(4-methoxy-3-oxidanyl-phenyl)methylidene]-1,3-thiazolidin-4-one / CGP 53820


Mass: 360.815 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13ClN2O3S / 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.: 325 / 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: 39.57 %
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: 1.55→58.91 Å / Num. obs: 46044 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.026 / Rrim(I) all: 0.066 / Χ2: 0.95 / Net I/σ(I): 16.2 / Num. measured all: 291627
Reflection shellResolution: 1.55→1.58 Å / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.731 / Num. measured all: 14516 / Num. unique obs: 2254 / CC1/2: 0.824 / Rpim(I) all: 0.311 / Rrim(I) all: 0.796 / Χ2: 0.94 / Net I/σ(I) obs: 2.7

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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: 1.55→36.502 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1921 2314 5.03 %
Rwork0.1639 --
obs0.1653 46012 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→36.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 48 325 3146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062921
X-RAY DIFFRACTIONf_angle_d0.8413954
X-RAY DIFFRACTIONf_dihedral_angle_d15.4541736
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 (%)
1.55-1.58170.26411350.22742531X-RAY DIFFRACTION100
1.5817-1.6160.27531270.21612557X-RAY DIFFRACTION100
1.616-1.65360.21471310.1982594X-RAY DIFFRACTION100
1.6536-1.6950.24031430.18712546X-RAY DIFFRACTION100
1.695-1.74080.22581140.18762556X-RAY DIFFRACTION100
1.7408-1.7920.2071240.18612575X-RAY DIFFRACTION100
1.792-1.84990.1951370.18242577X-RAY DIFFRACTION100
1.8499-1.9160.19231340.17382558X-RAY DIFFRACTION100
1.916-1.99270.20841200.1762547X-RAY DIFFRACTION100
1.9927-2.08340.21031440.16642590X-RAY DIFFRACTION100
2.0834-2.19320.19271470.16972553X-RAY DIFFRACTION100
2.1932-2.33060.19491570.16482555X-RAY DIFFRACTION100
2.3306-2.51050.1871450.16882556X-RAY DIFFRACTION100
2.5105-2.76310.20421360.1692580X-RAY DIFFRACTION100
2.7631-3.16270.19691700.16042540X-RAY DIFFRACTION100
3.1627-3.98390.17551260.14082618X-RAY DIFFRACTION100
3.9839-36.5020.16031240.15132665X-RAY DIFFRACTION99
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)
10.13240.0808-0.0388-0.0022-0.07570.4408-0.10710.0858-0.22920.01650.0687-0.15280.10380.04-00.19550.00910.02350.1691-0.07110.283215.1837-24.7153-48.0674
20.3980.24970.08830.15720.12550.440.01790.0402-0.03190.0579-0.0203-0.0667-0.05540.0615-00.1455-0.0038-0.01270.1762-0.01710.181319.5815-10.7725-45.7032
30.91970.0273-0.52010.37760.00580.4934-0.00660.12870.00110.0450.0248-0.0493-0.0054-0.10270.00130.13480.011-0.00910.1264-0.00340.1145-3.9594-13.0551-41.9124
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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