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- PDB-8c6n: Human protein kinase CK2 alpha in complex with CK2-TN03 -

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Basic information

Entry
Database: PDB / ID: 8c6n
TitleHuman protein kinase CK2 alpha in complex with CK2-TN03
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 / molecular replacement / Resolution: 2.05 Å
AuthorsDalle Vedove, A. / Cazzanelli, G. / Lolli, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
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. / Aiello, G. / Ruzzene, M. / Tiberi, L. / Fava, L. / Quattrone, A. / Lolli, G.
History
DepositionJan 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2024Provider: 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)40,7685
Polymers40,1541
Non-polymers6154
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-47 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.492, 46.518, 63.434
Angle α, β, γ (deg.)90.000, 111.840, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 40153.820 Da / Num. of mol.: 1 / Fragment: kinase domain (residues 1-337)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-TN0 / (2~{Z},5~{Z})-5-[(4-methoxy-3-oxidanyl-phenyl)methylidene]-2-phenylimino-1,3-thiazolidin-4-one


Mass: 326.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.99 Å3/Da / Density % sol: 38.34 % / Mosaicity: 0.41 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / 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: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→46.52 Å / Num. obs: 20099 / % possible obs: 99.8 % / Redundancy: 5.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.069 / Rrim(I) all: 0.164 / Net I/σ(I): 8.6 / Num. measured all: 110893 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1 / Redundancy: 5.4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.05-2.110.831844815550.7550.3890.9212.299.7
8.94-46.520.05314602680.9970.0240.0592599.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.11.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q04

3q04


Resolution: 2.05→36.501 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2182 954 4.75 %
Rwork0.1785 19113 -
obs0.1805 20067 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.8 Å2 / Biso mean: 29.4105 Å2 / Biso min: 12.24 Å2
Refinement stepCycle: final / Resolution: 2.05→36.501 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 38 235 3046
Biso mean--33.9 33.97 -
Num. residues----328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072897
X-RAY DIFFRACTIONf_angle_d0.9423923
X-RAY DIFFRACTIONf_chiral_restr0.057403
X-RAY DIFFRACTIONf_plane_restr0.005501
X-RAY DIFFRACTIONf_dihedral_angle_d6.122419
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0501-2.15810.2941390.24582694100
2.1581-2.29330.30291300.23132726100
2.2933-2.47040.24681270.20252711100
2.4704-2.71890.24991370.19742712100
2.7189-3.11210.25481410.1852739100
3.1121-3.92020.17861350.1545273399
3.9202-36.5010.17651450.15112798100
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)
10.4219-0.01880.1150.0705-0.19960.5351-0.14090.0824-0.2205-0.05980.0821-0.16070.18550.0683-0.00020.29480.01260.02340.2923-0.08670.366315.61-24.7164-47.8875
21.00530.10240.36240.76910.64460.62040.0302-0.1137-0.12310.1713-0.0335-0.15670.10070.10920.00030.22380.0021-0.02480.2831-0.04160.315522.8322-14.0794-45.2846
30.1049-0.06110.03780.0393-0.02040.0127-0.2322-0.21180.36770.41370.2962-0.0045-0.2872-0.17570.00140.34280.06690.01110.3006-0.01210.437211.7652-1.282-47.289
41.6555-0.1197-0.4721.0716-0.14780.9933-0.0470.1051-0.0020.06030.0446-0.0521-0.0212-0.11430.00010.18360.0103-0.01750.1669-0.01860.1571-3.6527-13.0617-41.8582
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 44 )A3 - 44
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 108 )A45 - 108
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 129 )A109 - 129
4X-RAY DIFFRACTION4chain 'A' and (resid 130 through 330 )A130 - 330

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