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- PDB-5m4f: Complex structure of human protein kinase CK2 catalytic subunit w... -

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Basic information

Entry
Database: PDB / ID: 5m4f
TitleComplex structure of human protein kinase CK2 catalytic subunit with the inhibitor 4'-carboxy-6,8-chloro-flavonol (FLC21) 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 / 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 / Maturation of hRSV A proteins ...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 / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of signal transduction by p53 class mediator / 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 / 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 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-7FC / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.519 Å
AuthorsNiefind, K. / Bischoff, N. / Yarmoluk, S.M. / Bdzhola, V.G. / Golub, A.G. / Balanda, A.O. / Prykhod'ko, A.O.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationNI 643/4-2 Germany
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)40,7657
Polymers40,0671
Non-polymers6986
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-24 kcal/mol
Surface area15550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.033, 79.569, 82.142
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-7FC / 4-[6,8-bis(chloranyl)-3-oxidanyl-4-oxidanylidene-chromen-2-yl]benzoic acid


Mass: 351.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H8Cl2O5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 37.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PROTEIN STOCK SOLUTION: 6 MG/ML 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/ML 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 % PEG3350, 0.2 M KCl; DROP SOLUTION BEFORE EQULIBRATION: 0.5 MICROLITER PROTEIN/INHIBITOR COMPLEX SOLUTION + 0.5 MICROLITER RESERVOIR SOLUTION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.519→41.5 Å / Num. obs: 49151 / % possible obs: 100 % / Redundancy: 4.1 % / Biso Wilson estimate: 15.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05914 / Rsym value: 0.05914 / Net I/σ(I): 15.82
Reflection shellResolution: 1.519→1.574 Å / Redundancy: 4 % / Rmerge(I) obs: 0.7874 / Mean I/σ(I) obs: 1.89 / CC1/2: 0.661 / % possible all: 99

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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: 3NSZ

3nsz


Resolution: 1.519→41.464 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.25
RfactorNum. reflection% reflection
Rfree0.1826 1031 2.1 %
Rwork0.1628 --
obs0.1632 49147 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.519→41.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2788 0 43 384 3215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142943
X-RAY DIFFRACTIONf_angle_d1.293987
X-RAY DIFFRACTIONf_dihedral_angle_d17.4421766
X-RAY DIFFRACTIONf_chiral_restr0.085409
X-RAY DIFFRACTIONf_plane_restr0.009511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5194-1.59950.27061320.23986785X-RAY DIFFRACTION99
1.5995-1.69970.22841300.19736769X-RAY DIFFRACTION100
1.6997-1.83090.19551550.17836805X-RAY DIFFRACTION100
1.8309-2.01520.17251600.1586831X-RAY DIFFRACTION100
2.0152-2.30670.17281610.14636837X-RAY DIFFRACTION100
2.3067-2.90610.21211390.16196928X-RAY DIFFRACTION100
2.9061-41.47960.15891540.15327161X-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)
11.24341.5389-0.07131.902-0.10280.2316-0.16970.15750.448-0.26350.05730.2913-0.126-0.16060.29430.2310.0079-0.00930.16680.00040.197-2.447211.1219-25.8072
22.52550.52650.13212.5963-0.50093.21950.0202-0.20320.10190.10570.0407-0.1464-0.08290.003-0.09050.13310.0227-0.00840.1408-0.02410.1768-21.7325-5.5524-14.1732
31.73540.18180.11440.70690.13260.69070.0007-0.0122-0.0531-0.01320.00720.07630.0194-0.1038-0.02640.12940.0046-0.00890.0771-0.01280.1131-6.9602-3.9155-15.1976
40.71270.13230.14980.67840.26910.6750.0237-0.12420.00920.0787-0.02440.0016-0.0053-0.02560.00850.10640.00190.00340.0671-0.01740.08840.23855.3902-6.4218
51.07920.04350.0781.2530.18411.41810.0441-0.22850.05750.24570.0008-0.1703-0.0590.1616-0.01350.1622-0.0276-0.03170.1723-0.01840.145712.41078.51391.1834
60.5395-0.4344-0.22752.83740.24772.379-0.00150.1802-0.2617-0.2312-0.0069-0.03950.30480.015-0.00230.12030.0086-0.00920.0874-0.02250.177414.0872-9.0534-13.5289
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 35 )
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 74 )
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 149 )
4X-RAY DIFFRACTION4chain 'A' and (resid 150 through 249 )
5X-RAY DIFFRACTION5chain 'A' and (resid 250 through 314 )
6X-RAY DIFFRACTION6chain 'A' and (resid 315 through 331 )

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