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- PDB-8q77: STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALP... -

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Basic information

Entry
Database: PDB / ID: 8q77
TitleSTRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 GENE PRODUCT) IN COMPLEX WITH THE BISUBSTRATE INHIBITOR ARC-780
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE / protein kinase CK2 casein kinase 2 bisubstrate inhibitor N-terminal segment ligand binding site
Function / homology
Function and homology information


regulation of mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins ...regulation of mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / 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 / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / acrosomal vesicle / Signal transduction by L1 / liver regeneration / cerebral cortex development / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / chromatin / nucleoplasm / ATP binding / nucleus / 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
Chem-LN3 / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.255 Å
AuthorsWerner, C. / Lindenblatt, D. / Niefind, K.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/11-1 Germany
German Research Foundation (DFG)NI 643/4-2 Germany
Citation
Journal: Kinases Phosphatases / Year: 2023
Title: Discovery and Exploration of Protein Kinase CK2 Binding Sites Using CK2alpha Cys336Ser as an Exquisite Crystallographic Tool
Authors: Werner, C. / Lindenblatt, D. / Viht, K. / Uri, A. / Niefind, K.
#1: Journal: ACS Omega / Year: 2019
Title: Diacritic Binding of an Indenoindole Inhibitor by CK2alpha Paralogs Explored by a Reliable Path to Atomic Resolution CK2alpha' Structures.
Authors: Lindenblatt, D. / Nickelsen, A. / Applegate, V.M. / Hochscherf, J.
History
DepositionAug 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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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)45,13010
Polymers42,8801
Non-polymers2,2509
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint7 kcal/mol
Surface area16430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.603, 47.919, 51.031
Angle α, β, γ (deg.)66.590, 89.670, 88.160
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 42879.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A2, CK2A2 / Production host: Escherichia coli (E. coli)
References: UniProt: P19784, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-LN3 / (2~{S})-2-[[(2~{S})-2-[[(2~{S})-2-[12-[[4-[[5-(4-carboxyphenyl)-1,3-thiazol-2-yl]amino]-4-oxidanylidene-butanoyl]-(2-hydroxy-2-oxoethyl)amino]dodecanoylamino]-4-oxidanyl-4-oxidanylidene-butanoyl]amino]-4-oxidanyl-4-oxidanylidene-butanoyl]amino]butanedioic acid


Mass: 920.936 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H52N6O17S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: THE CK2ALPHA' SOLUTION AFTER PROTEIN PURIFICATION (5 MG/ML CK2ALPHA' IN 500 MM NACL, 25 MM TRIS/HCl, PH 8.5) WAS MIXED IN 1:10 VOLUME RATIO WITH 10 MM SOLUTION OF THE INHIBITOR MB002 IN DMSO. ...Details: THE CK2ALPHA' SOLUTION AFTER PROTEIN PURIFICATION (5 MG/ML CK2ALPHA' IN 500 MM NACL, 25 MM TRIS/HCl, PH 8.5) WAS MIXED IN 1:10 VOLUME RATIO WITH 10 MM SOLUTION OF THE INHIBITOR MB002 IN DMSO. THIS SOLUTION WAS MIXED IN 2:1 RATIO WITH RESERVOIR SOLUTION [900 MM LICL, 28 % (W/V) PEG 6000, 250 MM TRIS/HCL, PH 8.5] IN SITTING DROP PLATES (VAPOUR DIFFUSION). THE CRYSTAL GROWTH WAS INDUCED BY MICROSEEDING. THE CRYSTALS WERE OPTIMIZED BY MACROSEEDING AND PURGED TWICE WITH RESERVOIR SOLUTION. THEN, ARC-780 WAS ADDED TO AN INITIAL CONCENTRATION OF 1 MM BY ADDING 1 MIKROLITER OF A 10 MM ARC-780 SOLUTION IN DMSO IN A 1:10 RATIO TO THE DROPLET. AFTER EXTENSIVE INTIAL SOAKING, THE SALT CONCENTRATION WAS SUCCESSIVELY LOWERED OVER A PERIOD OF 8 MONTHS WHILE IN PARALLEL THE CONCENTRATIONS OF DMSO AND PEG 6000 WERE INCREASED. THIS WAS DONE BY GRADUALLY REPLACING THE RESERVOIR AND THE DROPLET SOLUTION UNTIL ANY NACL WAS REMOVED, THE LICL CONCENTRATION WAS REDUCED TO 50 MM, THE PEG 6000 CONCENTRATION WAS INCREASED TO SATURATION AND A DMSO CONTENT OF 30% WAS REACHED. MEANWHILE, THE ARC-780 LIGAND WAS INCLUDED IN ANY DESALTING STEP REACHING SATURATION AFTER THE FINAL DILUTION STEP. ALL STEPS WERE PERFORMED AT A TEMPERATURE OF 293 K.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.255→46.578 Å / Num. obs: 80300 / % possible obs: 72.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 10.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.031 / Rrim(I) all: 0.061 / Rsym value: 0.052 / Net I/σ(I): 12.2
Reflection shellResolution: 1.255→1.364 Å / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4015 / CC1/2: 0.806 / Rpim(I) all: 0.326 / Rrim(I) all: 0.648 / Rsym value: 0.559

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.255→41.25 Å / SU ML: 0.0864 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 16.9147
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.157 1214 1.51 %
Rwork0.1197 79069 -
obs0.1202 80283 72.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.47 Å2
Refinement stepCycle: LAST / Resolution: 1.255→41.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 153 311 3232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0233016
X-RAY DIFFRACTIONf_angle_d1.77154058
X-RAY DIFFRACTIONf_chiral_restr0.1415408
X-RAY DIFFRACTIONf_plane_restr0.0183524
X-RAY DIFFRACTIONf_dihedral_angle_d18.29811159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.255-1.310.382110.2711714X-RAY DIFFRACTION5.88
1.31-1.360.2404440.18813299X-RAY DIFFRACTION27.15
1.36-1.440.21041210.14738124X-RAY DIFFRACTION67.16
1.44-1.530.18311840.115511161X-RAY DIFFRACTION92.3
1.53-1.640.14591770.10311309X-RAY DIFFRACTION92.55
1.64-1.810.12451680.092211172X-RAY DIFFRACTION92.39
1.81-2.070.13171680.094811012X-RAY DIFFRACTION91.03
2.07-2.610.14411490.113610330X-RAY DIFFRACTION84.95
2.61-41.250.17241920.139311948X-RAY DIFFRACTION98.72

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