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- PDB-4uba: Low-salt structure of protein kinase CK2 catalytic subunit with 4... -

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Basic information

Entry
Database: PDB / ID: 4uba
TitleLow-salt structure of protein kinase CK2 catalytic subunit with 4'-carboxy-6,8-bromo-flavonol (FLC26)
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / protein kinase CK2 / ATP-competitive inhibitors / halogen bond / 4'-carboxy-6 / 8-bromo-flavonol
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 / Synthesis of PC / Sin3-type complex / 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 / Synthesis of PC / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of signal transduction by p53 class mediator / 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 / : / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / PML body / Regulation of PTEN stability and activity / Wnt signaling pathway / positive regulation of protein catabolic process / kinase activity / KEAP1-NFE2L2 pathway / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / DNA damage response / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-3G5 / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.995 Å
AuthorsNiefind, K. / Bischoff, N. / Guerra, B. / Golub, A. / Issinger, O.-G.
Citation
Journal: Acs Chem.Biol. / Year: 2015
Title: A Note of Caution on the Role of Halogen Bonds for Protein Kinase/Inhibitor Recognition Suggested by High- And Low-Salt CK2 alpha Complex Structures.
Authors: Guerra, B. / Bischoff, N. / Bdzhola, V.G. / Yarmoluk, S.M. / Issinger, O.G. / Golub, A.G. / Niefind, K.
#1: Journal: Mol. Cell. Biochem. / Year: 2011
Title: Structure-based discovery of novel flavonol inhibitors of human protein kinase CK2.
Authors: Golub, A.G. / Bdzhola, V.G. / Kyshenia, Y.V. / Sapelkin, V.M. / Prykhod'ko, A.O. / Kukharenko, O.P. / Ostrynska, O.V. / Yarmoluk, S.M.
#2: 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.
#3: Journal: EMBO J. / Year: 2001
Title: Crystal structure of human protein kinase CK2: insights into basic properties of the CK2 holoenzyme.
Authors: Niefind, K. / Guerra, B. / Ermakowa, I. / Issinger, O.G.
History
DepositionAug 12, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)81,0144
Polymers80,1332
Non-polymers8802
Water81145
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5072
Polymers40,0671
Non-polymers4401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5072
Polymers40,0671
Non-polymers4401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.000, 126.000, 124.140
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 / Fragment: UNP residues 1-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Plasmid: pT7-7 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-3G5 / 4-(6,8-dibromo-3-hydroxy-4-oxo-4H-chromen-2-yl)benzoic acid


Mass: 440.040 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H8Br2O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: Reservoir: 30 %(w/v) PEG4000, 0.2 M ammonium acetate, 0.1 M trisodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.995→44.55 Å / Num. obs: 20425 / % possible obs: 98.5 % / Redundancy: 6.5 % / Rsym value: 0.172 / Net I/σ(I): 10.6

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.995→44.548 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2386 1018 5 %
Rwork0.1872 --
obs0.1897 20353 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.995→44.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5624 0 46 45 5715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025824
X-RAY DIFFRACTIONf_angle_d0.5527880
X-RAY DIFFRACTIONf_dihedral_angle_d10.4162192
X-RAY DIFFRACTIONf_chiral_restr0.023810
X-RAY DIFFRACTIONf_plane_restr0.0031012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9953-3.15320.29981300.27432460X-RAY DIFFRACTION90
3.1532-3.35070.27511450.22632758X-RAY DIFFRACTION100
3.3507-3.60930.28921460.20282758X-RAY DIFFRACTION100
3.6093-3.97230.22711450.17342764X-RAY DIFFRACTION100
3.9723-4.54670.22881470.15632791X-RAY DIFFRACTION100
4.5467-5.72640.20951500.16392834X-RAY DIFFRACTION100
5.7264-44.55260.22461550.19512970X-RAY DIFFRACTION100
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)
15.51641.24332.28361.42630.6973.24680.0302-0.31-0.15290.1503-0.00290.1238-0.057-0.238-0.07220.5284-0.01330.02310.4625-0.00460.2003-4.0247-48.377817.8831
22.55851.4437-2.85642.2166-3.52925.7389-0.65071.04430.1216-1.62510.0617-0.0213-0.3735-0.80520.16531.1744-0.1623-0.09180.7890.19540.4711-4.1995-40.14360.9043
33.24710.42040.20081.519-0.11272.7253-0.07850.38950.0472-0.43580.11530.0112-0.07580.1517-0.04330.6242-0.12530.02930.45-0.00760.230114.6481-38.21656.4448
40.4708-0.7376-0.10684.571.22631.43940.0064-0.0637-0.03380.0594-0.0261-0.07730.1245-0.0387-0.02240.56750.0580.04740.57360.0460.2245-15.0645-65.647446.3705
58.6246-4.55263.17353.7195-0.20323.34120.94892.66290.0249-0.9373-1.3647-0.30560.01291.16290.51171.15110.2185-0.19061.313-0.15470.6944-27.5592-64.049126.9751
61.8518-0.4247-0.16552.6164-0.23152.34240.21130.13760.0461-0.4726-0.08990.0566-0.2963-0.0806-0.12870.66850.14050.00010.4759-0.00020.2349-26.0786-46.457336.1509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 108 )
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 334 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 113 )
5X-RAY DIFFRACTION5chain 'B' and (resid 114 through 129 )
6X-RAY DIFFRACTION6chain 'B' and (resid 130 through 334 )

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