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- PDB-8qf1: STRUCTURE OF THE CATALYTIC SUBUNIT OF PROTEIN KINASE CK2 (CK2ALPH... -

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Basic information

Entry
Database: PDB / ID: 8qf1
TitleSTRUCTURE OF THE CATALYTIC SUBUNIT OF PROTEIN KINASE CK2 (CK2ALPHA') IN COMPLEX WITH THE NON-HYDROLYZABLE GTP ANALOGUE GMPPNP
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE
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 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 / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / cell cycle / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 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. / Witulski, B. / Bouaziz, Z. / Marminon, C. / Bretner, M. / Le Borgne, M. / Jose, J. / Niefind, K.
History
DepositionSep 1, 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'
B: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3556
Polymers85,7602
Non-polymers5954
Water10,935607
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.628, 71.590, 102.101
Angle α, β, γ (deg.)90.000, 92.090, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 42879.867 Da / Num. of mol.: 2
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-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10 MIKROLITER CK2ALPHA' SOLUTION AFTER PROTEIN PURIFICATION (5 MG/ML CK2ALPHA' IN 500 MM NACL, 25 MM TRIS/HCl, PH 8.5) WERE MIXED WITH 5 MIKROLITER RESERVOIR SOLUTION [810 MM LICL, 28% (W/V) ...Details: 10 MIKROLITER CK2ALPHA' SOLUTION AFTER PROTEIN PURIFICATION (5 MG/ML CK2ALPHA' IN 500 MM NACL, 25 MM TRIS/HCl, PH 8.5) WERE MIXED WITH 5 MIKROLITER RESERVOIR SOLUTION [810 MM LICL, 28% (W/V) PEG 6000, 100 MM TRIS/HCL, PH 8.5]. AFTER EQUILIBRATION (SITTING DROP PLATES; VAPOUR DIFFUSION), CRYSTALLIZATION WAS INITIATED BY MICROSEEDING. THE CRYSTALS WERE OPTIMIZED BY MACROSEEDING. THE GTP-ANALOGUE GMPPNP WAS COMBINED WITH THESE CRYSTALS BY SOAKING. A 20 MM GMPPNP SOLUTION IN 60 MM MGCL2 WAS PREPARED. FOR SOAKING, 3 MICROLITER OF THE CRYSTAL MOTHER LIQUOR WAS REMOVED AND REPLACED BY 3 MICROLITER OF 20 MM GMPPNP, 60 MM MGCL2. 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: ID23-1 / Wavelength: 0.885603 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Sep 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885603 Å / Relative weight: 1
ReflectionResolution: 1.318→102.033 Å / Num. obs: 91444 / % possible obs: 57.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 12.8 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.088 / Rrim(I) all: 0.17 / Rsym value: 0.144 / Net I/σ(I): 4.1
Reflection shellResolution: 1.318→1.493 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4572 / CC1/2: 0.367 / Rpim(I) all: 0.327 / Rrim(I) all: 0.579 / Rsym value: 0.472 / % possible all: 9.3

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Processing

Software
NameVersionClassification
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→58.6 Å / SU ML: 0.1137 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.912
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2324 1370 1.5 %
Rwork0.2139 89975 -
obs0.2142 91345 57.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.67 Å2
Refinement stepCycle: LAST / Resolution: 1.32→58.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5485 0 35 607 6127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00375786
X-RAY DIFFRACTIONf_angle_d0.66647839
X-RAY DIFFRACTIONf_chiral_restr0.0618811
X-RAY DIFFRACTIONf_plane_restr0.00531006
X-RAY DIFFRACTIONf_dihedral_angle_d12.47362201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.360.987310.2997138X-RAY DIFFRACTION0.88
1.36-1.420.4088170.3214981X-RAY DIFFRACTION6.35
1.42-1.480.3420.29642857X-RAY DIFFRACTION18.46
1.48-1.560.2908720.27625096X-RAY DIFFRACTION32.8
1.56-1.660.2821350.25619100X-RAY DIFFRACTION58.54
1.66-1.790.23811950.240212141X-RAY DIFFRACTION77.95
1.79-1.970.24372180.225214349X-RAY DIFFRACTION92.5
1.97-2.250.20612320.201614968X-RAY DIFFRACTION95.97
2.25-2.840.2172240.208814990X-RAY DIFFRACTION95.98
2.84-58.60.23712340.203515355X-RAY DIFFRACTION97.04

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