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- PDB-3pe1: Crystal structure of human protein kinase CK2 alpha subunit in co... -

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Basic information

Entry
Database: PDB / ID: 3pe1
TitleCrystal structure of human protein kinase CK2 alpha subunit in complex with the inhibitor CX-4945
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-3NG / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
DepositionOct 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2012Group: Database references
Revision 1.2Sep 6, 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)40,8795
Polymers40,2411
Non-polymers6384
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.478, 46.087, 63.493
Angle α, β, γ (deg.)90.000, 111.590, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical ChemComp-3NG / 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid


Mass: 349.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H12ClN3O2 / Comment: chemotherapy, inhibitor*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 1.98 Å3/Da / Density % sol: 37.78 %
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: PILATUS 2M / Detector: PIXEL / Date: Jul 6, 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: 1.6→46.09 Å / Num. all: 41497 / Num. obs: 41165 / % possible obs: 99.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 17.74 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 24.7
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 4.1 / Num. unique all: 5905 / Rsym value: 0.466 / % possible all: 97.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.2_432refinement
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: 1.6→31.2 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8755 / SU ML: 0.19 / Isotropic thermal model: Isotropic + TLS parameters / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 2092 5.04 %RANDOM
Rwork0.1601 ---
obs0.1622 41165 99.18 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.254 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso max: 88.01 Å2 / Biso mean: 24.8938 Å2 / Biso min: 7.92 Å2
Baniso -1Baniso -2Baniso -3
1--5.2877 Å20 Å2-0.3024 Å2
2--4.8362 Å2-0 Å2
3---0.4515 Å2
Refinement stepCycle: LAST / Resolution: 1.6→31.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2765 0 40 392 3197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052896
X-RAY DIFFRACTIONf_angle_d0.9873924
X-RAY DIFFRACTIONf_chiral_restr0.074402
X-RAY DIFFRACTIONf_plane_restr0.005500
X-RAY DIFFRACTIONf_dihedral_angle_d13.7321095
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 (%)
1.5988-1.65590.27962030.22213807401097
1.6559-1.72220.26252200.20639314151100
1.7222-1.80060.27412090.19523905411499
1.8006-1.89550.24472030.17533811401497
1.8955-2.01430.20461750.156740524227100
2.0143-2.16970.18481980.151639334131100
2.1697-2.3880.20292270.15739314158100
2.388-2.73340.20272020.16293978418099
2.7334-3.44310.20092270.159239744201100
3.4431-31.20570.17452280.143740564284100
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)
10.1150.1019-0.04010.08210.01180.0613-0.27420.2822-0.39050.0840.1448-0.20450.0094-0.24620.00110.2097-0.02260.060.1638-0.06180.272.091-54.560414.0828
20.05760.03240.09560.0708-0.02920.1962-0.25410.3196-0.3054-0.13170.1872-0.37320.07310.1017-0.00020.21130.03420.02820.2387-0.1590.393321.7729-55.02429.1839
30.8615-0.04150.40260.74640.57080.6063-0.05240.1145-0.02620.0139-0.14650.11830.00490.1455-00.1165-0.0221-0.00420.1873-0.0410.179132.2796-32.234214.4244
40.68020.41860.03750.36070.28620.3293-0.04730.1309-0.10550.03930.0197-0.16150.01980.097400.1099-0.0046-0.00830.1549-0.05540.175426.7866-39.846511.7627
50.7894-0.2964-0.16160.6322-0.6680.2346-0.13670.23850.09020.15470.1765-0.2533-0.0297-0.20190.0020.07520.0185-0.01350.1546-0.03130.07258.062-30.61898.0278
60.976-0.0513-0.3760.2103-0.26140.2583-0.04440.113-0.07940.02720.0196-0.0624-0.0088-0.00240.00010.11470.0066-0.00890.0825-0.02180.11399.9849-39.268816.8877
70.7595-0.5496-0.1860.3958-0.2180.7272-0.0966-0.02350.00680.18570.0129-0.0357-0.0359-0.048900.16650.0081-0.00910.08850.00140.0969-2.4746-38.075727.8991
80.2218-0.0781-0.03590.29270.22870.156-0.12820.03650.00770.09520.03530.15820.11090.0336-00.20650.03440.01710.15690.02490.1356-10.554-34.862828.7324
90.593-0.0802-0.1080.7474-0.11310.54680.0030.2468-0.00850.03660.01150.1122-0.0101-0.182500.09660.00190.00110.16620.01590.0877-4.3882-32.50910.1389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:14)A3 - 14
2X-RAY DIFFRACTION2(chain A and resid 15:32)A15 - 32
3X-RAY DIFFRACTION3(chain A and resid 33:74)A33 - 74
4X-RAY DIFFRACTION4(chain A and resid 75:118)A75 - 118
5X-RAY DIFFRACTION5(chain A and resid 119:153)A119 - 153
6X-RAY DIFFRACTION6(chain A and resid 154:224)A154 - 224
7X-RAY DIFFRACTION7(chain A and resid 225:269)A225 - 269
8X-RAY DIFFRACTION8(chain A and resid 270:282)A270 - 282
9X-RAY DIFFRACTION9(chain A and resid 283:329)A283 - 329

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