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

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Basic information

Entry
Database: PDB / ID: 8qcd
TitleSTRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 GENE PRODUCT) IN COMPLEX WITH THE INHIBITOR 4,5,6,7-TETRABROMOBENZOTRIAZOLE
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE / protein kinase CK2 casein kinase 2 inhibitor TBB
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
4,5,6,7-TETRABROMOBENZOTRIAZOLE / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 Å
AuthorsWerner, C. / 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.
#2: Journal: J Mol Biol / Year: 2011
Title: Structure of the human protein kinase CK2 catalytic subunit CK2alpha' and interaction thermodynamics with the regulatory subunit CK2beta
Authors: Bischoff, N. / Olsen, B. / Raaf, J. / Bretner, M. / Issinger, O. / Niefind, K.
History
DepositionAug 25, 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)43,5015
Polymers42,8801
Non-polymers6214
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint8 kcal/mol
Surface area14940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.338, 47.701, 50.342
Angle α, β, γ (deg.)113.480, 90.450, 90.170
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-TBS / 4,5,6,7-TETRABROMOBENZOTRIAZOLE / TETRABROMO-2-BENZOTRIAZOLE


Mass: 434.708 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6HBr4N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.61 Å3/Da / Density % sol: 52.88 %
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 A 1:10 RATIO WITH A 20 MM SOLUTION OF 4,5,6,7- ...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 A 1:10 RATIO WITH A 20 MM SOLUTION OF 4,5,6,7-TETRABROMOBENZOTRIAZOLE (TBBT) IN DMSO. AFTER INCUBATION ON ICE FOR 30 MIN AND CENTRIFUGATION (16100 TIMES G FOR 2 MIN AT ROOM TEMPERATUR) 10 MIKROLITER OF THE SUPERNATANT WERE MIXED WITH 5 MIKORLITER OF THE RESERVOIR SOLUTION [900 MM LICL, 28% (W/V) PEG 6000, 100 MM TRIS/HCl, PH 8.5]. AFTER EQUILIBRATION, MICROSEEDING WAS CARRIED OUT TO INDUCE CRYSTAL GROWTH. SMALL CRYSTALS APPEARED AFTER ONE WEEK. ONE OF THEM WAS USED AS A MACROSEED TRANSFERING IT TO A SECOND DROP PREPARED IN THE SAME MANNER AS THE FIRST ONE. ALL CRSTALLIZATION 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: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.03→46.336 Å / Num. obs: 149296 / % possible obs: 76.9 % / Redundancy: 2.6 % / Biso Wilson estimate: 1.45 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.128 / Net I/σ(I): 5.7
Reflection shellResolution: 1.033→1.07 Å / Num. unique obs: 2611 / CC1/2: 0.561

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Processing

Software
NameVersionClassification
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.03→24.92 Å / SU ML: 0.0472 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 13.1818
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1562 2014 1.35 %
Rwork0.1437 147251 -
obs0.1439 149265 76.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 7.66 Å2
Refinement stepCycle: LAST / Resolution: 1.03→24.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 25 397 3181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00942983
X-RAY DIFFRACTIONf_angle_d1.05174041
X-RAY DIFFRACTIONf_chiral_restr0.0906413
X-RAY DIFFRACTIONf_plane_restr0.0132524
X-RAY DIFFRACTIONf_dihedral_angle_d13.12311150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.03-1.060.3291220.2281502X-RAY DIFFRACTION10.98
1.06-1.090.2623380.2143380X-RAY DIFFRACTION24.72
1.09-1.120.226750.19585589X-RAY DIFFRACTION40.78
1.12-1.160.23221360.179412X-RAY DIFFRACTION68.82
1.16-1.20.15121630.149612167X-RAY DIFFRACTION88.85
1.2-1.240.13621830.134412482X-RAY DIFFRACTION91.78
1.24-1.30.13271670.130512723X-RAY DIFFRACTION92.73
1.3-1.370.15171710.122612784X-RAY DIFFRACTION93.5
1.37-1.460.14291860.11712816X-RAY DIFFRACTION93.75
1.46-1.570.12651720.114512781X-RAY DIFFRACTION93.68
1.57-1.730.13171790.121712884X-RAY DIFFRACTION94.06
1.73-1.980.1431730.132812752X-RAY DIFFRACTION93.35
1.98-2.490.16011780.140113071X-RAY DIFFRACTION95.51
2.49-24.920.15811710.169212908X-RAY DIFFRACTION94.2

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