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- PDB-6a1c: Crystal structure of the CK2a1-go289 complex -

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Basic information

Entry
Database: PDB / ID: 6a1c
TitleCrystal structure of the CK2a1-go289 complex
ComponentsCasein kinase II subunit alphaCasein kinase 2
KeywordsTRANSFERASE / CK2a1 / Inhibitor / Complex
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 / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / peptidyl-threonine phosphorylation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of protein catabolic process / rhythmic process / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / protein stabilization / regulation of cell cycle / non-specific serine/threonine protein kinase / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 ...Casein Kinase 2, subunit alpha / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-9NX / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsKinoshita, T. / Tsuyuguchi, M.
CitationJournal: Sci Adv / Year: 2019
Title: Cell-based screen identifies a new potent and highly selective CK2 inhibitor for modulation of circadian rhythms and cancer cell growth.
Authors: Oshima, T. / Niwa, Y. / Kuwata, K. / Srivastava, A. / Hyoda, T. / Tsuchiya, Y. / Kumagai, M. / Tsuyuguchi, M. / Tamaru, T. / Sugiyama, A. / Ono, N. / Zolboot, N. / Aikawa, Y. / Oishi, S. / ...Authors: Oshima, T. / Niwa, Y. / Kuwata, K. / Srivastava, A. / Hyoda, T. / Tsuchiya, Y. / Kumagai, M. / Tsuyuguchi, M. / Tamaru, T. / Sugiyama, A. / Ono, N. / Zolboot, N. / Aikawa, Y. / Oishi, S. / Nonami, A. / Arai, F. / Hagihara, S. / Yamaguchi, J. / Tama, F. / Kunisaki, Y. / Yagita, K. / Ikeda, M. / Kinoshita, T. / Kay, S.A. / Itami, K. / Hirota, T.
History
DepositionJun 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,53429
Polymers40,4781
Non-polymers2,05628
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint74 kcal/mol
Surface area15540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.657, 78.831, 79.403
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Casein kinase II subunit alpha / Casein kinase 2 / CK II alpha


Mass: 40478.191 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 (E. coli)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-9NX / 5-bromanyl-2-methoxy-4-[(E)-(3-methylsulfanyl-5-phenyl-1,2,4-triazol-4-yl)iminomethyl]phenol


Mass: 419.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15BrN4O2S
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 38.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: ethyleneglycol

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.68→55.95 Å / Num. obs: 37267 / % possible obs: 99.6 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 30.6
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 5.7 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3war

3war


Resolution: 1.68→55.94 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.409 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.1 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19627 1839 4.9 %RANDOM
Rwork0.13751 ---
obs0.14042 35376 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 23.406 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å2-0 Å2
2---1.37 Å2-0 Å2
3---2 Å2
Refinement stepCycle: 1 / Resolution: 1.68→55.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2817 0 130 186 3133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193001
X-RAY DIFFRACTIONr_bond_other_d0.0020.022875
X-RAY DIFFRACTIONr_angle_refined_deg1.9211.974006
X-RAY DIFFRACTIONr_angle_other_deg0.92436582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6015335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06523.057157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92315515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4371526
X-RAY DIFFRACTIONr_chiral_restr0.1210.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213278
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02732
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0511.0621337
X-RAY DIFFRACTIONr_mcbond_other2.0521.0621336
X-RAY DIFFRACTIONr_mcangle_it2.4391.5991670
X-RAY DIFFRACTIONr_mcangle_other2.4381.5991671
X-RAY DIFFRACTIONr_scbond_it3.3161.5451664
X-RAY DIFFRACTIONr_scbond_other3.2961.5451664
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5592.142336
X-RAY DIFFRACTIONr_long_range_B_refined3.88110.8873583
X-RAY DIFFRACTIONr_long_range_B_other3.85610.8333576
X-RAY DIFFRACTIONr_rigid_bond_restr6.20335876
X-RAY DIFFRACTIONr_sphericity_free26.536585
X-RAY DIFFRACTIONr_sphericity_bonded9.16255926
LS refinement shellResolution: 1.683→1.727 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 149 -
Rwork0.142 2463 -
obs--95.29 %
Refinement TLS params.Method: refined / Origin x: 11.6302 Å / Origin y: 10.5032 Å / Origin z: 17.8378 Å
111213212223313233
T0.0095 Å20.0062 Å20.0031 Å2-0.0259 Å20.0059 Å2--0.0144 Å2
L1.8321 °20.3561 °2-0.4668 °2-1.1628 °2-0.1739 °2--0.7048 °2
S0.0454 Å °0.0111 Å °0.1466 Å °-0.0252 Å °0.0135 Å °0.0703 Å °-0.0213 Å °-0.0486 Å °-0.0589 Å °

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