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- PDB-8c6l: Human protein kinase CK2 alpha in complex with CK2-TN01 -

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Basic information

Entry
Database: PDB / ID: 8c6l
TitleHuman protein kinase CK2 alpha in complex with CK2-TN01
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 / Sin3-type complex / Synthesis of PC / 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 / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / 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 / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / rhythmic process / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / protein stabilization / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / positive regulation of cell population proliferation / 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: 1.8 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)40,7856
Polymers40,1541
Non-polymers6325
Water6,413356
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)58.446, 46.362, 63.255
Angle α, β, γ (deg.)90.000, 112.020, 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-TO6 / 5-azanyl-3-[(~{Z})-1-cyano-2-(3-methoxy-4-oxidanyl-phenyl)ethenyl]-3~{H}-pyrazole-4-carbonitrile


Mass: 281.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11N5O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 356 / 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: 1.98 Å3/Da / Density % sol: 37.84 % / Mosaicity: 0.33 °
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: 1.8→46.36 Å / Num. obs: 29330 / % possible obs: 99.9 % / Redundancy: 4.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.042 / Rrim(I) all: 0.09 / Net I/σ(I): 11.5 / Num. measured all: 131102
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.840.724759817200.7280.390.8252.199.9
9-46.360.03911362590.9970.0210.04529.798.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q04

3q04


Resolution: 1.8→36.369 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 1436 4.9 %
Rwork0.1642 27870 -
obs0.1664 29306 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.68 Å2 / Biso mean: 26.1634 Å2 / Biso min: 10.86 Å2
Refinement stepCycle: final / Resolution: 1.8→36.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 40 356 3169
Biso mean--33.56 35.04 -
Num. residues----328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062907
X-RAY DIFFRACTIONf_angle_d0.83937
X-RAY DIFFRACTIONf_chiral_restr0.053405
X-RAY DIFFRACTIONf_plane_restr0.005503
X-RAY DIFFRACTIONf_dihedral_angle_d16.4491733
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.8-1.86440.32021510.25462761
1.8644-1.9390.26291510.21782728
1.939-2.02720.23951470.19432772
2.0272-2.13410.24091440.17762767
2.1341-2.26780.23411240.17472800
2.2678-2.44290.21481370.16752804
2.4429-2.68860.21631670.17022728
2.6886-3.07750.22881310.16082825
3.0775-3.87660.16261480.14332804
3.8766-36.3690.19011360.14712881
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)
11.97780.1132-1.20460.49740.67762.3846-0.2673-0.2331-0.41770.07720.20520.16960.48060.0653-0.02310.27120.02450.04830.1730.09680.2882-9.6814-9.1782-10.3474
21.587-0.925-0.02052.4272-0.45771.3382-0.1383-0.0574-0.2468-0.02030.1884-0.0020.1674-0.3685-0.02930.1618-0.0583-0.00270.24920.01920.2779-33.57026.3259-11.6326
31.9776-0.72230.6020.6968-0.59440.55660.0224-0.0062-0.0668-0.0477-0.00210.13330.0421-0.0683-0.01510.15890.0049-0.00380.22940.03380.2571-28.44649.0003-13.4015
41.66020.7359-0.12830.89860.62260.7262-0.154-0.14070.3192-0.11530.1850.2703-0.17330.1284-0.03990.1915-0.0194-0.01620.2070.0230.1994-11.828617.5518-8.0398
51.85750.1351-0.65570.8679-0.11340.7987-0.05860.0152-0.0136-0.13540.04210.08170.02480.0040.01160.1628-0.0126-0.02310.1220.00960.1209-3.79227.8985-21.6839
60.8084-0.055-0.14951.4850.14181.1474-0.008-0.2640.06-0.00480.0403-0.0086-0.09360.2764-0.04260.1383-0.0169-0.0010.2431-0.02470.15694.432414.3481-10.0061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 24 )A3 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 44 )A25 - 44
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 108 )A45 - 108
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 149 )A109 - 149
5X-RAY DIFFRACTION5chain 'A' and (resid 150 through 280 )A150 - 280
6X-RAY DIFFRACTION6chain 'A' and (resid 281 through 330 )A281 - 330

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