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- PDB-5n9n: Crystal structure of human Protein kinase CK2 catalytic subunit i... -

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Basic information

Entry
Database: PDB / ID: 5n9n
TitleCrystal structure of human Protein kinase CK2 catalytic subunit in complex with the ATP-competitive, tight-binding dibenzofuran inhibitor TF85 (4a)
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 / 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
ACETATE ION / Chem-KC5 / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.841 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 2.0May 22, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site / struct_site_gen
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Jan 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,22712
Polymers40,0671
Non-polymers1,16011
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-0 kcal/mol
Surface area15370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.477, 45.505, 63.489
Angle α, β, γ (deg.)90.00, 110.97, 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 / Fragment: UNP residues 1-335
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-KC5 / (4~{Z})-7,9-bis(chloranyl)-4-[[(4-methoxyphenyl)amino]methylidene]-8-oxidanyl-1,2-dihydrodibenzofuran-3-one


Mass: 404.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H15Cl2NO4
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 175 / 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: 36.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Prior to the crystallization the Inhibitor TF85 was solubilized in 100 % DMSO in a concentration of 10 mM. This TF85 stock solution was mixed with human CK2alpha (construct 1-335; Protein ...Details: Prior to the crystallization the Inhibitor TF85 was solubilized in 100 % DMSO in a concentration of 10 mM. This TF85 stock solution was mixed with human CK2alpha (construct 1-335; Protein concentration 8-10 mg/ml in 500 mM sodium chloride, 25 mM Tris/HCl pH 8.5) in a ratio of 1:10. 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 these mixtures were then equilibrated against the reservoir solution. The crystal growth was induced by seeding with 150 nanoliter seeding 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: 1.84→45.51 Å / Num. obs: 25795 / % possible obs: 96.4 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 12.6
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 3 % / Rmerge(I) obs: 0.75 / Num. unique obs: 1395 / CC1/2: 0.644 / Rsym value: 0.75 / % possible all: 84.2

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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: 1.841→34.165 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.35
RfactorNum. reflection% reflection
Rfree0.2011 1317 5.11 %
Rwork0.167 --
obs0.1686 25774 96.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.841→34.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 77 175 3031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032952
X-RAY DIFFRACTIONf_angle_d0.5683986
X-RAY DIFFRACTIONf_dihedral_angle_d13.1961746
X-RAY DIFFRACTIONf_chiral_restr0.044404
X-RAY DIFFRACTIONf_plane_restr0.005512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8405-1.91420.29071470.27032524X-RAY DIFFRACTION90
1.9142-2.00130.23551320.22652678X-RAY DIFFRACTION96
2.0013-2.10680.25421420.18992722X-RAY DIFFRACTION96
2.1068-2.23880.20991310.1762740X-RAY DIFFRACTION97
2.2388-2.41160.2051440.17172734X-RAY DIFFRACTION97
2.4116-2.65420.21191640.17842739X-RAY DIFFRACTION97
2.6542-3.03810.22531590.17332752X-RAY DIFFRACTION97
3.0381-3.82680.20151590.1482752X-RAY DIFFRACTION97
3.8268-34.17050.15671390.15032816X-RAY DIFFRACTION96
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)
13.0921-1.67330.27572.29390.04980.93230.0968-0.2322-0.47060.0109-0.05320.41080.1987-0.3858-0.02740.2775-0.0985-0.00170.43540.07830.3595-18.46343.232945.9685
25.24840.7051.33120.95780.67911.3515-0.1267-0.37860.2396-0.05120.08940.2635-0.0964-0.23380.0110.2490.02050.02570.32670.04470.2368-10.706113.765250.3736
32.8672-0.1543-0.48451.39280.27422.29340.02340.051-0.0101-0.1830.02190.0768-0.0399-0.0076-0.05240.2033-0.01-0.02610.15790.03620.17191.90817.236437.615
41.9106-0.33370.16023.66411.37032.7467-0.0521-0.12390.1012-0.010.141-0.1168-0.07190.2525-0.09540.1832-0.0121-0.00090.2409-0.00170.222510.663913.445248.7537
57.99692.5798-3.15764.3402-1.17159.55030.88319.7801-0.5114-0.4413-2.21842.7451-1.96596.21351.34350.87330.3647-0.18791.7716-0.16271.8161-2.986314.829165.7176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 87 )
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 149 )
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 280 )
4X-RAY DIFFRACTION4chain 'A' and (resid 281 through 329 )
5X-RAY DIFFRACTION5chain 'A' and (resid 330 through 330 )

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