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- PDB-5m4u: ORTHORHOMBIC COMPLEX STRUCTURE OF HUMAN PROTEIN KINASE CK2 CATALY... -

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Basic information

Entry
Database: PDB / ID: 5m4u
TitleORTHORHOMBIC COMPLEX STRUCTURE OF HUMAN PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA') WITH THE INHIBITOR 4'-CARBOXY-6,8-CHLORO- FLAVONOL (FLC21)
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2
Function / homology
Function and homology information


regulation of mitophagy / regulation of chromosome separation / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Synthesis of PC / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...regulation of mitophagy / regulation of chromosome separation / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Synthesis of PC / 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 / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / acrosomal vesicle / liver regeneration / Signal transduction by L1 / cerebral cortex development / Wnt signaling pathway / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / chromatin / nucleoplasm / ATP binding / nucleus / 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 / ACETATE ION / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.195 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 19, 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 2.0Oct 10, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_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)43,94212
Polymers42,8221
Non-polymers1,12011
Water5,675315
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-25 kcal/mol
Surface area15710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.850, 83.780, 142.344
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 42821.832 Da / Num. of mol.: 1 / Mutation: Asp39Gly, Cys336Ser
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A2, CK2A2 / Production host: Escherichia coli (E. coli)
References: UniProt: P19784, non-specific serine/threonine protein kinase

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Non-polymers , 6 types, 326 molecules

#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.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 3.32 Å3/Da / Density % sol: 62.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PROTEIN STOCK SOLUTION: 5.5 MG/ML CK2ALPHA'D39G-C336S 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 ...Details: PROTEIN STOCK SOLUTION: 5.5 MG/ML CK2ALPHA'D39G-C336S 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: 25 % PEG5000 MME, 0.2 M ammonium sulphate, 0.1 M MES buffer, pH 6.5; 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: 2.195→44.6 Å / Num. obs: 29246 / % possible obs: 99 % / Redundancy: 6.4 % / Biso Wilson estimate: 21.44 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1909 / Rsym value: 0.1909 / Net I/σ(I): 9.99
Reflection shellResolution: 2.195→2.274 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.185 / Mean I/σ(I) obs: 1.72 / CC1/2: 0.684 / % possible all: 93

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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: 3OFM

3ofm


Resolution: 2.195→44.502 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.03
RfactorNum. reflection% reflection
Rfree0.214 1142 3.91 %
Rwork0.1704 --
obs0.1721 28094 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.195→44.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 0 71 315 3171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032925
X-RAY DIFFRACTIONf_angle_d0.5763943
X-RAY DIFFRACTIONf_dihedral_angle_d15.7761739
X-RAY DIFFRACTIONf_chiral_restr0.043402
X-RAY DIFFRACTIONf_plane_restr0.003502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1953-2.29520.291400.26393256X-RAY DIFFRACTION94
2.2952-2.41620.24061380.20433502X-RAY DIFFRACTION100
2.4162-2.56750.23561380.17853480X-RAY DIFFRACTION100
2.5675-2.76580.26711330.18023511X-RAY DIFFRACTION100
2.7658-3.0440.24021500.17323486X-RAY DIFFRACTION100
3.044-3.48440.19521360.1533556X-RAY DIFFRACTION100
3.4844-4.38930.17031620.13623554X-RAY DIFFRACTION100
4.3893-44.51070.19741450.16923749X-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)
11.1914-0.2131-0.2470.65330.44760.9669-0.046-0.2706-0.03140.16740.0302-0.01670.05370.11070.00050.17690.00330.00640.22370.01580.16533.072-14.8249-11.4226
21.30360.1466-0.03970.8480.10860.7755-0.02620.06630.0046-0.03840.0365-0.04450.0006-0.0207-0.00370.1125-0.0043-0.00330.09860.00570.101314.9445-13.2497-30.2894
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 130 )
2X-RAY DIFFRACTION2chain 'A' and (resid 131 through 334 )

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