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- PDB-9i11: Human protein kinase CK2 alpha in complex with TN16 -

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Basic information

Entry
Database: PDB / ID: 9i11
TitleHuman protein kinase CK2 alpha in complex with TN16
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 / KEAP1-NFE2L2 pathway / kinase activity / 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: 1.6 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)40,1558
Polymers39,3041
Non-polymers8517
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-48 kcal/mol
Surface area15510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.484, 46.630, 63.303
Angle α, β, γ (deg.)90.00, 111.59, 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-A1IYW / (2~{Z},5~{Z})-2-(3-hydroxyphenyl)imino-5-[(4-methoxy-3-oxidanyl-phenyl)methylidene]-1,3-thiazolidin-4-one


Mass: 342.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14N2O4S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 39.77 %
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: 1.6→58.86 Å / Num. obs: 41951 / % possible obs: 99.7 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.019 / Rrim(I) all: 0.047 / Χ2: 0.93 / Net I/σ(I): 19.3 / Num. measured all: 255811
Reflection shellResolution: 1.6→1.63 Å / % possible obs: 98.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.567 / Num. measured all: 9943 / Num. unique obs: 2063 / CC1/2: 0.796 / Rpim(I) all: 0.285 / Rrim(I) all: 0.639 / Χ2: 0.86 / Net I/σ(I) obs: 2.5

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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: 1.6→36.55 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1959 2054 4.9 %
Rwork0.1635 --
obs0.1651 41924 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→36.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 52 253 3078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062921
X-RAY DIFFRACTIONf_angle_d0.8483956
X-RAY DIFFRACTIONf_dihedral_angle_d15.9261735
X-RAY DIFFRACTIONf_chiral_restr0.055405
X-RAY DIFFRACTIONf_plane_restr0.005504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.63720.28051280.22852610X-RAY DIFFRACTION99
1.6372-1.67820.2291390.20742655X-RAY DIFFRACTION100
1.6782-1.72360.25821410.20132653X-RAY DIFFRACTION100
1.7236-1.77430.21651380.18892641X-RAY DIFFRACTION100
1.7743-1.83150.22841440.18552622X-RAY DIFFRACTION99
1.8315-1.8970.21771480.17352609X-RAY DIFFRACTION100
1.897-1.97290.21231340.17782684X-RAY DIFFRACTION100
1.9729-2.06270.19861360.16522626X-RAY DIFFRACTION100
2.0627-2.17150.19971380.16412659X-RAY DIFFRACTION99
2.1715-2.30750.17221280.16992662X-RAY DIFFRACTION100
2.3075-2.48560.20091430.16582646X-RAY DIFFRACTION100
2.4856-2.73570.22571190.17282702X-RAY DIFFRACTION100
2.7357-3.13140.19541470.16822666X-RAY DIFFRACTION100
3.1314-3.94440.17531320.14812695X-RAY DIFFRACTION100
3.9444-36.550.18161390.14762740X-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)
10.53950.18770.09560.0708-0.02820.4269-0.05730.0393-0.1180.0350.0208-0.11480.10780.1464-00.20220.00890.0060.2345-0.06330.27518.8826-18.4065-46.2684
20.30370.2139-0.03590.1247-0.02870.4022-0.08420.02510.03660.13790.0662-0.1722-0.17230.0934-0.00010.20490.02-0.03590.2114-0.03640.248117.3213-11.9897-46.9551
30.9229-0.0159-0.46660.3803-0.01940.7512-0.00160.12680.00360.06340.033-0.04590.0016-0.109600.17090.016-0.00660.1598-0.0050.1543-3.8553-13.0178-41.7912
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 330 )

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