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- PDB-5m4c: Complex structure of human protein kinase CK2 catalytic subunit w... -

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Basic information

Entry
Database: PDB / ID: 5m4c
TitleComplex structure of human protein kinase CK2 catalytic subunit with a thieno[2,3-d]pyrimidin inhibitor crystallized under low-salt conditions
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2
Function / homology
Function and homology information


regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins ...regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / 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 / 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 / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H2AS121 kinase activity / histone H3S57 kinase activity / histone H3S28 kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / ribosomal protein S6 kinase activity / histone H2AT120 kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / histone H2BS36 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H3S10 kinase activity / AMP-activated protein kinase activity / histone H3T11 kinase activity / histone H3T3 kinase activity / 3-phosphoinositide-dependent protein kinase activity / histone H3T45 kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / KEAP1-NFE2L2 pathway / kinase activity / 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 phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / 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-7EY / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.935 Å
AuthorsNiefind, K. / Bischoff, N. / Yarmoluk, S.M. / Bdzhola, V.G. / Golub, A.G. / Balanda, A.O. / Prykhod'ko, A.O.
Funding support1items
OrganizationGrant numberCountry
German Research FoundationNI 643/4-2
Citation
Journal: Pharmaceuticals / Year: 2017
Title: Structural Hypervariability of the Two Human Protein Kinase CK2 Catalytic Subunit Paralogs Revealed by Complex Structures with a Flavonol- and a Thieno[2,3-d]pyrimidine-Based Inhibitor.
Authors: Niefind, K. / Bischoff, N. / Golub, A.G. / Bdzhola, V.G. / Balanda, A.O. / Prykhod'ko, A.O. / Yarmoluk, S.M.
#1: 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 CK2alpha Complex Structures.
Authors: Guerra, B. / Bischoff, N. / Bdzhola, V.G. / Yarmoluk, S.M. / Issinger, O.G. / Golub, A.G. / Niefind, K.
#2: Journal: Eur J Med Chem / Year: 2011
Title: Synthesis and biological evaluation of substituted (thieno[2,3-d]pyrimidin-4-ylthio)carboxylic acids as inhibitors of human protein kinase CK2.
Authors: Golub, A.G. / Bdzhola, V.G. / Briukhovetska, N.V. / Balanda, A.O. / Kukharenko, O.P. / Kotey, I.M. / Ostrynska, O.V. / Yarmoluk, S.M.
#3: 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.
History
DepositionOct 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2May 10, 2017Group: Database references
Revision 1.3May 17, 2017Group: Database references
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6175
Polymers40,0671
Non-polymers5504
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-14 kcal/mol
Surface area15490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.104, 79.418, 82.341
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 40066.742 Da / Num. of mol.: 1
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-7EY / 3-[5-(4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]sulfanylpropanoic acid


Mass: 330.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14N2O2S2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 1.96 Å3/Da / Density % sol: 37.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PROTEIN STOCK SOLUTION: 6 MG/M CK2ALPHA1-335 IN 0.5 M NACL, 25 MM TRIS/HCL, PH 8.5; INHIBITOR STOCK SOLUTION: 10 MM INHIBITOR IN DMSO; PROTEIN/INHIBITOR COMPLEX SOLUTION: 90 MICROLITER ...Details: PROTEIN STOCK SOLUTION: 6 MG/M CK2ALPHA1-335 IN 0.5 M NACL, 25 MM TRIS/HCL, PH 8.5; INHIBITOR STOCK SOLUTION: 10 MM INHIBITOR IN DMSO; PROTEIN/INHIBITOR COMPLEX SOLUTION: 90 MICROLITER PROTEIN STOCK SOLUTION + 10 MICROLITER INHIBITOR STOCK SOLUTION; RESERVOIR SOLUTION: 24 % (w/v) PEG8000, 0.2 M KCl; DROP SOLUTION BEFORE EQULIBRATION: 0.3 MICROLITER PROTEIN/INHIBITOR COMPLEX SOLUTION + 0.3 MICROLITER RESERVOIR SOLUTION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / 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: 1.935→41.6 Å / Num. obs: 23281 / % possible obs: 96 % / Redundancy: 6.3 % / Biso Wilson estimate: 21.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0982 / Rsym value: 0.0982 / Net I/σ(I): 15.25
Reflection shellResolution: 1.935→2.004 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.7305 / Mean I/σ(I) obs: 2.26 / CC1/2: 0.758 / % possible all: 62

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PVR

2pvr


Resolution: 1.935→41.535 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.89
RfactorNum. reflection% reflection
Rfree0.1968 1104 4.74 %
Rwork0.1565 --
obs0.1584 23281 96.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.935→41.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2782 0 35 228 3045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092919
X-RAY DIFFRACTIONf_angle_d1.0313950
X-RAY DIFFRACTIONf_dihedral_angle_d16.2761750
X-RAY DIFFRACTIONf_chiral_restr0.059406
X-RAY DIFFRACTIONf_plane_restr0.006507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9351-2.02320.2701970.20661957X-RAY DIFFRACTION70
2.0232-2.12980.21041430.18132836X-RAY DIFFRACTION100
2.1298-2.26330.24281390.17312848X-RAY DIFFRACTION100
2.2633-2.4380.21491410.16432847X-RAY DIFFRACTION100
2.438-2.68330.22351280.16132864X-RAY DIFFRACTION100
2.6833-3.07150.20131490.15962880X-RAY DIFFRACTION100
3.0715-3.86930.17361400.1362915X-RAY DIFFRACTION100
3.8693-41.5450.1721670.14823030X-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)
13.5856-0.130.13915.52111.25670.91070.02710.60270.2142-0.40750.14720.2778-0.34910.0719-0.02430.2891-0.02660.04040.22120.05240.19914.443112.8448-24.8878
22.02030.9172-0.11223.5759-0.09052.1265-0.02710.41850.2054-0.51530.1246-0.273-0.413-0.3014-0.02270.29870.03610.03230.23950.01710.2508-20.5072-0.5973-23.1657
33.34740.91840.62934.7048-0.76073.28080.174-0.290.31560.052-0.0858-0.0741-0.3743-0.168-0.06320.18530.00170.00520.1717-0.03750.2123-20.4376-4.1763-14.0103
42.99011.4842-0.22531.41680.1081.4317-0.06440.29540.4689-0.1603-0.00610.3204-0.3335-0.41940.05050.22890.0455-0.04620.24070.00890.2153-14.59061.9412-22.4149
52.01430.05120.42132.0003-0.14161.0320.038-0.1962-0.18440.1534-0.0196-0.02440.0861-0.0478-0.02580.161-0.008-0.0050.1015-0.01680.099-2.0268-6.6087-10.5116
61.47860.45340.00410.67650.3391.75530.0555-0.05130.1348-0.01440.00570.0808-0.1494-0.0292-0.02080.1270.0070.01380.0882-0.03560.10990.8447.3946-9.6131
72.54640.9077-0.09673.62980.00053.23960.0023-0.24950.22820.3130.1028-0.2354-0.30790.0937-0.04160.2019-0.02610.00510.2136-0.08120.17578.121214.13553.9917
81.8199-0.15530.54383.79690.24971.17980.0605-0.289-0.15710.5468-0.0017-0.30750.0560.1944-0.04370.217-0.0046-0.03440.2518-0.00890.194113.3764-0.7802-0.4765
94.6518-0.56810.03341.8027-1.60896.50240.02650.5059-0.3495-0.1972-0.0947-0.19950.33550.27610.01940.14990.0154-0.00120.2026-0.05010.183413.7893-9.1664-13.6827
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 44 )
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 74 )
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 108 )
5X-RAY DIFFRACTION5chain 'A' and (resid 109 through 168 )
6X-RAY DIFFRACTION6chain 'A' and (resid 169 through 227 )
7X-RAY DIFFRACTION7chain 'A' and (resid 228 through 280 )
8X-RAY DIFFRACTION8chain 'A' and (resid 281 through 314 )
9X-RAY DIFFRACTION9chain 'A' and (resid 315 through 331 )

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