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- PDB-3r0t: Crystal structure of human protein kinase CK2 alpha subunit in co... -

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Basic information

Entry
Database: PDB / ID: 3r0t
TitleCrystal structure of human protein kinase CK2 alpha subunit in complex with the inhibitor CX-5279
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase / CK2-inhibitor complex / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / Sin3-type complex / Synthesis of PC / 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 / Sin3-type complex / Synthesis of PC / 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 ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / double-strand break repair / rhythmic process / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / protein stabilization / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / positive regulation of cell population proliferation / 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-FU9 / DI(HYDROXYETHYL)ETHER / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBattistutta, R. / Papinutto, E. / Lolli, G. / Pierre, F. / Haddach, M. / Ryckman, D.M.
Citation
Journal: Biochemistry / Year: 2011
Title: Unprecedented selectivity and structural determinants of a new class of protein kinase CK2 inhibitors in clinical trials for the treatment of cancer.
Authors: Battistutta, R. / Cozza, G. / Pierre, F. / Papinutto, E. / Lolli, G. / Sarno, S. / O'Brien, S.E. / Siddiqui-Jain, A. / Haddach, M. / Anderes, K. / Ryckman, D.M. / Meggio, F. / Pinna, L.A.
#1: Journal: Biochem.J. / Year: 2009
Title: Quinalizarin as a potent, selective and cell-permeable inhibitor of protein kinase CK2.
Authors: Cozza, G. / Mazzorana, M. / Papinutto, E. / Bain, J. / Elliott, M. / di Maira, G. / Gianoncelli, A. / Pagano, M.A. / Sarno, S. / Ruzzene, M. / Battistutta, R. / Meggio, F. / Moro, S. / Zagotto, G. / Pinna, L.A.
History
DepositionMar 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Structure summary
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)41,72916
Polymers40,2411
Non-polymers1,48815
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.352, 46.184, 63.300
Angle α, β, γ (deg.)90.000, 111.510, 90.000
Int Tables number4
Space group name H-MP1211

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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: 40240.902 Da / Num. of mol.: 1 / Fragment: unp residues 1-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli)
References: UniProt: P68400, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 349 molecules

#2: Chemical ChemComp-FU9 / 3-(cyclopropylamino)-5-{[3-(trifluoromethyl)phenyl]amino}pyrimido[4,5-c]quinoline-8-carboxylic acid / CX-5279


Mass: 439.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H16F3N5O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 1.97 Å3/Da / Density % sol: 37.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 32% PEG 4000, 0.2M Li2SO4, 0.1M Tris pH 8.5, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 30, 2010 / Details: Mirrors
RadiationMonochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→46.18 Å / Num. all: 28551 / Num. obs: 28551 / % possible obs: 89.6 % / Redundancy: 2.8 % / Biso Wilson estimate: 17.833 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.75-1.841.60.4621.7410426190.46257.4
1.84-1.962.10.2692.8741635450.26981.3
1.96-2.092.60.1923.9997037750.19291.8
2.09-2.2630.1594.61138337430.15997.8
2.26-2.473.20.1225.81104835010.12299.4
2.47-2.773.20.1026.71035732210.10299.5
2.77-3.23.30.0818916028090.08199.5
3.2-3.913.30.0688.8789524050.06899.6
3.91-5.533.30.0629.3614718730.06299.8
5.53-46.1843.30.05410.8347710600.05499.2

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data processing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
ElettraXRD1 in house softwaredata collection
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2PVR

2pvr


Resolution: 1.75→35.177 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8521 / SU ML: 0.2 / Isotropic thermal model: Isotropic + TLS parameters / σ(F): 0 / Phase error: 22.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2107 1420 4.98 %RANDOM
Rwork0.1602 ---
obs0.1628 28526 89.44 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.791 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso max: 88.21 Å2 / Biso mean: 24.0662 Å2 / Biso min: 6.73 Å2
Baniso -1Baniso -2Baniso -3
1--6.3098 Å20 Å2-1.1651 Å2
2--3.4799 Å2-0 Å2
3---2.8299 Å2
Refinement stepCycle: LAST / Resolution: 1.75→35.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2765 0 95 334 3194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072946
X-RAY DIFFRACTIONf_angle_d1.0363976
X-RAY DIFFRACTIONf_chiral_restr0.075406
X-RAY DIFFRACTIONf_plane_restr0.005501
X-RAY DIFFRACTIONf_dihedral_angle_d13.6081109
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.81260.3005820.23851548163051
1.8126-1.88520.22791130.20412123223671
1.8852-1.9710.2351290.18252580270985
1.971-2.07490.22781400.16622782292292
2.0749-2.20480.22571450.16382927307297
2.2048-2.3750.22171520.16543009316199
2.375-2.6140.25411790.17252975315499
2.614-2.9920.24291530.166230333186100
2.992-3.7690.18941620.14563026318899
3.769-35.18420.16871650.14373103326899
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)
10.05640.02430.00830.0078-0.00030.015-0.0120.0526-0.0471-0.00620.086-0.0703-0.0106-0.046600.1667-0.05410.03530.1553-0.05650.20011.4641-55.614614.6268
20.0139-0.01270.03110.0999-0.00740.0686-0.24880.1931-0.1999-0.02110.0957-0.12430.18080.1616-00.21840.02350.05360.147-0.08580.344620.9593-56.55478.8193
30.0751-0.01170.08790.10450.02550.1087-0.07320.0348-0.0756-0.0804-0.19050.2135-0.02760.0701-0.00010.1317-0.02560.00880.2292-0.0750.231933.0192-34.068115.6464
40.0728-0.032-0.0050.01270.00350.0385-0.04610.14320.2397-0.13830.06260.05890.0279-0.07980.00070.1156-0.018-0.03530.2072-0.00430.129532.1118-31.591411.3104
50.17910.16410.00260.23260.10890.117-0.0039-0.1009-0.18520.09150.028-0.10440.06180.0149-00.12170.0066-0.0140.1772-0.02660.159724.7116-44.479611.8194
60.05-0.0064-0.00060.0814-0.14270.2482-0.00480.0020.24930.08020.0149-0.1391-0.0785-0.04400.13120.0178-0.00680.1502-0.00570.17815.9998-29.181910.8388
70.57520.0653-0.18330.47-0.28460.2096-0.04280.1121-0.04820.02530.0386-0.10520.0006-0.017400.0934-0.002-0.00270.0745-0.01970.10549.9353-41.394715.1453
80.1356-0.07980.06740.0378-0.04660.0555-0.07720.00270.15970.11550.0023-0.1846-0.0997-0.0487-0.00030.15490.0151-0.01510.08050.00120.10550.756-31.98726.3692
90.4401-0.1399-0.20050.2274-0.02760.3372-0.01030.1025-0.01260.01640.0378-0.01720.0227-0.13200.092-0.0082-0.00360.10090.01070.0675-5.9085-37.965418.3039
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:13)A3 - 13
2X-RAY DIFFRACTION2(chain A and resid 14:32)A14 - 32
3X-RAY DIFFRACTION3(chain A and resid 33:51)A33 - 51
4X-RAY DIFFRACTION4(chain A and resid 52:71)A52 - 71
5X-RAY DIFFRACTION5(chain A and resid 72:102)A72 - 102
6X-RAY DIFFRACTION6(chain A and resid 103:139)A103 - 139
7X-RAY DIFFRACTION7(chain A and resid 140:224)A140 - 224
8X-RAY DIFFRACTION8(chain A and resid 225:247)A225 - 247
9X-RAY DIFFRACTION9(chain A and resid 248:329)A248 - 329

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