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- PDB-5owl: Low salt structure of human protein kinase CK2alpha in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5owl
TitleLow salt structure of human protein kinase CK2alpha in complex with 3-aminopropyl-4,5,6,7-tetrabromobenzimidazol
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / protein kinase CK2 casein kinase 2 ATP-competitive inhibitor 3-aminopropyl-4 / 5 / 6 / 7-tetrabromobenzimidazol
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 / Maturation of hRSV A proteins / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / rhythmic process / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / protein stabilization / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / 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-B0K / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsNiefind, K. / Bretner, M. / Chojnacki, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationNI 643/4-2 Germany
Citation
Journal: Bioorg. Chem. / Year: 2018
Title: Biological properties and structural study of new aminoalkyl derivatives of benzimidazole and benzotriazole, dual inhibitors of CK2 and PIM1 kinases.
Authors: Chojnacki, K. / Winska, P. / Wielechowska, M. / Lukowska-Chojnacka, E. / Tolzer, C. / Niefind, K. / Bretner, M.
#1: Journal: Mol. Cell. Biochem. / Year: 2011
Title: Enzymatic activity with an incomplete catalytic spine: insights from a comparative structural analysis of human CK2alpha and its paralogous isoform CK2alpha'
Authors: Bischoff, N. / Raaf, J. / Olsen, B. / Bretner, M. / Issinger, O.G. / 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.G. / Niefind, K.
#3: Journal: J. Mol. Biol. / Year: 2003
Title: Crystal structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit.
Authors: Ermakova, I. / Boldyreff, B. / Issinger, O.G. / Niefind, K.
History
DepositionSep 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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

Downloads & links

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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)81,68810
Polymers80,1332
Non-polymers1,5548
Water2,234124
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7504
Polymers40,0671
Non-polymers6833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9386
Polymers40,0671
Non-polymers8715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.364, 126.364, 125.271
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 40066.742 Da / Num. of mol.: 2
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-B0K / 3-[4,5,6,7-tetrakis(bromanyl)benzimidazol-1-yl]propan-1-amine


Mass: 490.815 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9Br4N3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 3.12 Å3/Da / Density % sol: 60.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1 MIKROLITER OF THE CK2ALPHA/INHIBITOR MIXTURE (COMPOSITION: 7 MG/ML CK2ALPHA ENZYME, 1 MILLIMOLAR INHIBITOR, 10 % DIMETHYL SULFOXIDE, 450 MM NACL, 22.5 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 1 ...Details: 1 MIKROLITER OF THE CK2ALPHA/INHIBITOR MIXTURE (COMPOSITION: 7 MG/ML CK2ALPHA ENZYME, 1 MILLIMOLAR INHIBITOR, 10 % DIMETHYL SULFOXIDE, 450 MM NACL, 22.5 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 1 MIKROLITER RESERVOIR SOLUTION (COMPOSITION: 25 % PEG3350, 0.2 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS BUFFER, PH 5.5) FOLLOWED BY VAPOUR DIFFUSION EQUILIBRATION AGAINST THE RESERVOIR SOLUTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.966 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.23→72.75 Å / Num. obs: 49867 / % possible obs: 99.75 % / Redundancy: 6 % / Biso Wilson estimate: 52.58 Å2 / Rmerge(I) obs: 0.09056 / Rsym value: 0.09056 / Net I/σ(I): 12.78
Reflection shellResolution: 2.23→2.31 Å / Redundancy: 6.1 % / Rmerge(I) obs: 2.437 / Mean I/σ(I) obs: 0.81 / Num. unique obs: 4898 / CC1/2: 0.426 / Rsym value: 2.437 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5cqu

5cqu


Resolution: 2.23→63.182 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.44
RfactorNum. reflection% reflection
Rfree0.2488 1226 2.46 %
Rwork0.2105 --
obs0.2114 49832 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.23→63.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5597 0 65 124 5786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025820
X-RAY DIFFRACTIONf_angle_d0.4987876
X-RAY DIFFRACTIONf_dihedral_angle_d13.2563463
X-RAY DIFFRACTIONf_chiral_restr0.043808
X-RAY DIFFRACTIONf_plane_restr0.0031007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.31930.37891460.3285295X-RAY DIFFRACTION100
2.3193-2.42490.36051820.3075257X-RAY DIFFRACTION100
2.4249-2.55270.34531250.28285343X-RAY DIFFRACTION100
2.5527-2.71260.28331310.25965339X-RAY DIFFRACTION100
2.7126-2.92210.29251330.24285369X-RAY DIFFRACTION100
2.9221-3.21610.29651260.22465395X-RAY DIFFRACTION100
3.2161-3.68150.28411060.20635437X-RAY DIFFRACTION100
3.6815-4.63810.18571670.17295446X-RAY DIFFRACTION100
4.6381-63.20730.22651100.19255725X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0836-0.0475-0.04610.113-0.06980.15450.0764-0.6287-0.04520.3913-0.1091-0.1134-0.37070.40580.00070.6021-0.0571-0.08370.6262-0.00210.562813.6154-41.367627.8116
21.2602-0.2235-0.04910.458-0.29430.55140.0425-0.3281-0.3120.3308-0.08340.0811-0.2316-0.39680.01070.3546-0.0047-0.04280.4041-0.01090.5148-8.721-50.707414.8265
31.89530.573-0.33051.1608-0.13051.6065-0.05490.42080.0354-0.33780.1028-0.0856-0.00420.0383-0.00020.5978-0.0642-0.02860.47-0.01120.532513.5391-38.97746.0128
40.1747-0.1204-0.00360.3270.10970.0389-0.2137-0.4645-0.05710.57030.23960.0628-0.451-0.1706-0.00140.62450.0390.01970.6269-0.02250.5793-20.7858-48.520257.8511
50.74030.1285-0.29630.32220.420.6467-0.0706-0.0109-0.1420.30390.1712-0.260.63150.3465-0.00010.84220.0623-0.02370.56050.03270.5557-11.8048-71.850241.7859
60.161-0.2874-0.22060.42440.38820.2977-0.3435-0.1657-0.07920.31920.13080.65290.195-0.2285-0.00080.4081-0.00810.01240.3880.02330.4799-13.4734-68.387445.1205
70.06010.16350.07830.39130.18560.2196-0.3732-0.22210.21740.39560.1363-0.15110.13390.09610.00020.45310.0239-0.05030.60940.04360.604-15.1796-70.757846.0187
81.036-0.624-0.18951.0328-0.61730.83680.07620.2085-0.1164-0.3409-0.04130.11040.10530.0413-0.00010.62650.0735-0.04210.5774-0.00880.5652-23.263-52.775136.6798
90.1756-0.0866-0.06920.0789-0.03750.36380.11060.22580.8274-0.1904-0.1289-0.1434-0.71470.2646-00.76180.01750.05070.62380.08330.7196-18.1836-30.021735.6453
100.1785-0.150.04620.1074-0.0330.0133-0.04530.2541-0.0082-0.5899-0.12350.5630.14840.0212-0.00020.71040.1155-0.12540.63110.03050.5441-35.6083-43.69626.3257
110.1371-0.0262-0.19920.16220.03660.26410.1124-0.11920.0069-0.1659-0.13890.2499-0.3364-0.1013-0.00020.61230.1003-0.0120.6322-0.00260.7199-37.0859-48.299540.8148
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 108 )
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 332 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 24 )
5X-RAY DIFFRACTION5chain 'B' and (resid 25 through 58 )
6X-RAY DIFFRACTION6chain 'B' and (resid 59 through 87 )
7X-RAY DIFFRACTION7chain 'B' and (resid 88 through 108 )
8X-RAY DIFFRACTION8chain 'B' and (resid 109 through 249 )
9X-RAY DIFFRACTION9chain 'B' and (resid 250 through 280 )
10X-RAY DIFFRACTION10chain 'B' and (resid 281 through 304 )
11X-RAY DIFFRACTION11chain 'B' and (resid 305 through 333 )

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