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- PDB-5n9l: Crystal structure of human Protein kinase CK2 catalytic subunit i... -

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Basic information

Entry
Database: PDB / ID: 5n9l
TitleCrystal structure of human Protein kinase CK2 catalytic subunit in complex with the ATP-competitive dibenzofuran inhibitor TF (4b)
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / Protein kinase / CK2 / Casein kinase 2 / Protein phosphorylation / ATP-competitive inhititors / dibenzofuran derivatives / TIGHT-BINDING INHIBITORS
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 / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...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 / 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 proteasomal ubiquitin-dependent protein catabolic process / : / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / 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 / rhythmic process / double-strand break repair / kinase activity / peptidyl-serine phosphorylation / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / positive regulation of cell population proliferation / apoptotic process / 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-8QH / ACETATE ION / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsSchnitzler, A. / Gratz, A. / Bollacke, A. / Weyrich, M. / Kucklaender, U. / Wuensch, B. / Goetz, C. / Niefind, K. / Jose, J.
Citation
Journal: Pharmaceuticals / Year: 2018
Title: A pi-Halogen Bond of Dibenzofuranones with the Gatekeeper Phe113 in Human Protein Kinase CK2 Leads to Potent Tight Binding Inhibitors.
Authors: Schnitzler, A. / Gratz, A. / Bollacke, A. / Weyrich, M. / Kucklander, U. / Wunsch, B. / Gotz, C. / Niefind, K. / Jose, J.
#1: 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.
#2: Journal: J. Mol. Biol. / Year: 2005
Title: Inclining the purine base binding plane in protein kinase CK2 by exchanging the flanking side-chains generates a preference for ATP as a cosubstrate.
Authors: Yde, C.W. / Ermakova, I. / Issinger, O.G. / Niefind, K.
#3: Journal: Pharmaceuticals (Basel) / 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.
#4: Journal: Biochim. Biophys. Acta / Year: 2012
Title: TF--a novel cell-permeable and selective inhibitor of human protein kinase CK2 induces apoptosis in the prostate cancer cell line LNCaP.
Authors: Goetz, C. / Gratz, A. / Kucklaender, U. / Jose, J.
History
DepositionFeb 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / Item: _citation.country / _citation.journal_id_ISSN
Revision 1.3Apr 25, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_abbrev
Revision 1.4Jan 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)40,9418
Polymers40,0671
Non-polymers8757
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint1 kcal/mol
Surface area15440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.437, 45.706, 63.187
Angle α, β, γ (deg.)90.00, 110.94, 90.00
Int Tables number4
Space group name H-MP1211

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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-8QH / (4~{Z})-6,7-bis(chloranyl)-4-[[(4-methylphenyl)amino]methylidene]-8-oxidanyl-1,2-dihydrodibenzofuran-3-one


Mass: 388.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H15Cl2NO3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 1.93 Å3/Da / Density % sol: 36.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Prior to the crystallization TF was solubilized in 100 % DMSO in a concentration of 10 mM. TF was mixed with human CK2alpha (construct 1-335; 8-10 mg/ml in 500 mM sodium chloride, 25 mM ...Details: Prior to the crystallization TF was solubilized in 100 % DMSO in a concentration of 10 mM. TF was mixed with human CK2alpha (construct 1-335; 8-10 mg/ml in 500 mM sodium chloride, 25 mM Tris/HCl pH 8.5) in a ratio of 1:5. After a short time of incubation this mixture was mixed with reservoir solution [32 % (w/v) PEG4000, 0.2 M ammonium acetate, 0.1 M citrate pH 5.6] in a ratio of 5:2. 3.5 microliter of the resulting mixture was then equilibrated against the reservoir solution. The crystal growth was induced by seeding with 150 nanoliter seed suspension after an equilibration time of two days.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.79→36.14 Å / Num. obs: 27738 / % possible obs: 95.1 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 11.3
Reflection shellResolution: 1.79→1.83 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1127 / CC1/2: 0.76 / Rsym value: 0.545 / % possible all: 65.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PVR

2pvr


Resolution: 1.79→36.135 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.34
RfactorNum. reflection% reflection
Rfree0.1992 1389 5.01 %
Rwork0.1635 --
obs0.1653 27726 95.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.79→36.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 58 218 3055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032954
X-RAY DIFFRACTIONf_angle_d0.6643998
X-RAY DIFFRACTIONf_dihedral_angle_d12.6711754
X-RAY DIFFRACTIONf_chiral_restr0.045406
X-RAY DIFFRACTIONf_plane_restr0.005515
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7901-1.85410.28261140.23922174X-RAY DIFFRACTION79
1.8541-1.92830.26821400.20492642X-RAY DIFFRACTION96
1.9283-2.01610.19781310.19362660X-RAY DIFFRACTION97
2.0161-2.12230.23351590.17512620X-RAY DIFFRACTION96
2.1223-2.25530.23571170.17372653X-RAY DIFFRACTION96
2.2553-2.42940.21511460.17332681X-RAY DIFFRACTION97
2.4294-2.67380.21891450.17152658X-RAY DIFFRACTION97
2.6738-3.06050.21191300.17072741X-RAY DIFFRACTION98
3.0605-3.85520.18381370.14442738X-RAY DIFFRACTION98
3.8552-36.14270.16671700.14812770X-RAY DIFFRACTION98
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)
13.4446-1.85950.26162.0929-0.33890.5566-0.0008-0.1983-0.4108-0.01390.10520.4420.1112-0.2015-0.10080.2301-0.04940.00740.33820.04450.3428-18.39453.042346.0867
22.1458-0.1187-0.06090.8376-0.00471.22020.0142-0.11310.0766-0.05940.00390.2159-0.098-0.1454-0.01950.15470.0148-0.01050.1480.01750.1682-5.07610.609943.8001
31.21460.19740.12492.21171.03432.4436-0.00560.0315-0.0159-0.12440.0724-0.0916-0.03490.2024-0.06850.15730.0072-0.00830.20080.01080.206111.59429.735441.2006
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 88 )
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 249 )
3X-RAY DIFFRACTION3chain 'A' and (resid 250 through 330 )

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