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- PDB-8q9s: STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALP... -

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Basic information

Entry
Database: PDB / ID: 8q9s
TitleSTRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 GENE PRODUCT) IN COMPLEX WITH THE INHIBITOR SGC-CK2-1
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE / protein kinase CK2 casein kinase 2 inhibitor SGC-CK2-1
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 / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...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 / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of apoptotic signaling pathway / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / liver regeneration / acrosomal vesicle / Signal transduction by L1 / cerebral cortex development / Regulation of PTEN stability and activity / Wnt signaling pathway / KEAP1-NFE2L2 pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / 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 / DNA damage response / 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-QBE / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.352 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
CitationJournal: 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.
History
DepositionAug 21, 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)43,3794
Polymers42,8801
Non-polymers5003
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint6 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.217, 47.682, 50.562
Angle α, β, γ (deg.)66.830, 89.430, 88.930
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-QBE / ~{N}-[5-[[3-cyano-7-(cyclopropylamino)-3~{H}-pyrazolo[1,5-a]pyrimidin-5-yl]amino]-2-methyl-phenyl]propanamide


Mass: 375.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N7O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.62 Å3/Da / Density % sol: 53.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
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. A CRYSTAL WAS PURGED TWICE WITH RESERVOIR SOLUTION BEFORE ADDING SGC-CK2-1 (10 MM IN DMSO) TO A FINAL CONCENTRATION OF 2.5 MM TO THE CRYSTAL MOTHOR LIQUOR FOR EXTENSIVE SOAKING AND REPLACEMENT OF THE INITIAL INHIBITOR MB002 BY SGC-CK2-1. 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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.352→46.483 Å / Num. obs: 56703 / % possible obs: 65.3 % / Redundancy: 7.2 % / Biso Wilson estimate: 19.46 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.057 / Rrim(I) all: 0.104 / Rsym value: 0.097 / Net I/σ(I): 7.8
Reflection shellResolution: 1.352→1.519 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.482 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2835 / CC1/2: 0.589 / Rpim(I) all: 0.594 / Rrim(I) all: 1.598 / Rsym value: 1.482 / % possible all: 11.1

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Processing

Software
NameVersionClassification
autoPROC1.20.1_4487data processing
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.352→32.72 Å / SU ML: 0.1211 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.0636
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1688 1989 3.51 %
Rwork0.1354 54699 -
obs0.1366 56688 65.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.58 Å2
Refinement stepCycle: LAST / Resolution: 1.352→32.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 36 243 3038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082940
X-RAY DIFFRACTIONf_angle_d0.88583981
X-RAY DIFFRACTIONf_chiral_restr0.0762409
X-RAY DIFFRACTIONf_plane_restr0.0101509
X-RAY DIFFRACTIONf_dihedral_angle_d13.39321113
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.352-1.390.092250.2502113X-RAY DIFFRACTION1.91
1.39-1.420.165270.245303X-RAY DIFFRACTION5.09
1.42-1.460.2475310.2413727X-RAY DIFFRACTION12.17
1.46-1.510.2497520.21991320X-RAY DIFFRACTION22.21
1.51-1.570.2364860.20342453X-RAY DIFFRACTION40.91
1.57-1.630.25581440.18883927X-RAY DIFFRACTION65.41
1.63-1.70.2331890.16365087X-RAY DIFFRACTION84.69
1.7-1.790.22172030.15325652X-RAY DIFFRACTION95.13
1.79-1.90.17952130.12755816X-RAY DIFFRACTION96.56
1.9-2.050.15252100.1145772X-RAY DIFFRACTION96.81
2.05-2.260.1422200.10795830X-RAY DIFFRACTION97.39
2.26-2.590.14962030.12025857X-RAY DIFFRACTION97.81
2.59-3.260.16272170.13665911X-RAY DIFFRACTION98.52
3.26-32.720.16662090.14055931X-RAY DIFFRACTION98.98

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