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- PDB-5clp: Crystal Structure of CK2alpha with 3,4-dichlorophenethylamine bound -

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Basic information

Entry
Database: PDB / ID: 5clp
TitleCrystal Structure of CK2alpha with 3,4-dichlorophenethylamine bound
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / CK2alpha / CK2a / fragment based drug discovery / high concentration screening / selective ATP competitive inhibitors / surface entrophy reduction
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 / Maturation of hRSV A proteins ...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 / 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 / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / Signal transduction by L1 / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / peptidyl-threonine phosphorylation / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / peptidyl-serine phosphorylation / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / protein stabilization / regulation of cell cycle / non-specific serine/threonine protein kinase / negative regulation of translation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / DNA damage response / apoptotic process / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain / Protein kinase, ATP binding site ...Casein Kinase 2, subunit alpha / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase 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
2-(3,4-dichlorophenyl)ethanamine / ACETATE ION / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.684 Å
AuthorsBrear, P. / De Fusco, C. / Georgiou, K.H. / Spring, D. / Hyvonen, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust090340/Z/09/Z United Kingdom
CitationJournal: Chem Sci / Year: 2016
Title: Specific inhibition of CK2 alpha from an anchor outside the active site.
Authors: Brear, P. / De Fusco, C. / Hadje Georgiou, K. / Francis-Newton, N.J. / Stubbs, C.J. / Sore, H.F. / Venkitaraman, A.R. / Abell, C. / Spring, D.R. / Hyvonen, M.
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Data collection / Category: diffrn_radiation_wavelength / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 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
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,20316
Polymers82,9362
Non-polymers2,26814
Water8,071448
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7269
Polymers41,4681
Non-polymers1,2598
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4777
Polymers41,4681
Non-polymers1,0096
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.038, 69.025, 334.347
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 41467.793 Da / Num. of mol.: 2 / Fragment: UNP residues 2-329 / Mutation: R21S
Source method: isolated from a genetically manipulated source
Details: N-terminal extension GSMDIEFDDDADDDGSGSGSGSGS / Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Plasmid: pHAT4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-42J / 2-(3,4-dichlorophenyl)ethanamine


Mass: 190.070 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Formula: C8H9Cl2N
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 107mM Mes pH 6.5, 29% glycerol ethoxylate, 1 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.684→167.17 Å / Num. obs: 85744 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 24.35 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.033 / Rsym value: 0.077 / Net I/σ(I): 14.3 / Num. measured all: 564270
Reflection shellResolution: 1.684→1.689 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.877 / Mean I/σ(I) obs: 2.2 / Num. measured all: 82905 / Num. unique all: 12373 / CC1/2: 0.841 / Rpim(I) all: 0.311 / Rsym value: 0.877 / Rejects: 0 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER-TNTrefinement
Aimless0.2.14data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WAR

3war


Resolution: 1.684→167.17 Å / Cor.coef. Fo:Fc: 0.9546 / Cor.coef. Fo:Fc free: 0.9474 / SU R Cruickshank DPI: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.098 / SU Rfree Blow DPI: 0.089 / SU Rfree Cruickshank DPI: 0.088
RfactorNum. reflection% reflectionSelection details
Rfree0.1933 4331 5.06 %RANDOM
Rwork0.1778 ---
obs0.1785 85644 98.39 %-
Displacement parametersBiso max: 144.86 Å2 / Biso mean: 31.89 Å2 / Biso min: 7.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.7204 Å20 Å20 Å2
2---4.4803 Å20 Å2
3---3.76 Å2
Refine analyzeLuzzati coordinate error obs: 0.201 Å
Refinement stepCycle: final / Resolution: 1.684→167.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5471 0 188 448 6107
Biso mean--47.65 40.17 -
Num. residues----649
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2091SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes145HARMONIC2
X-RAY DIFFRACTIONt_gen_planes987HARMONIC5
X-RAY DIFFRACTIONt_it5942HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion700SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7120SEMIHARMONIC0
X-RAY DIFFRACTIONt_bond_d5942HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8044HARMONIC20.88
X-RAY DIFFRACTIONt_omega_torsion3.27
X-RAY DIFFRACTIONt_other_torsion16.19
LS refinement shellResolution: 1.684→1.72 Å
RfactorNum. reflection% reflection
Rfree0.2336 232 4.63 %
Rwork0.2183 4781 -
obs--98.39 %
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)
11.62060.19470.61390.06760.19530.87160.0727-0.33160.0072-0.0873-0.0192-0.0680.0931-0.2247-0.0535-0.0256-0.03010.0057-0.01550.0069-0.0815-6.6585156.146396.553
20.20690.06640.0620.3242-0.11070.62550.0132-0.0065-0.0192-0.00240.0003-0.0113-0.0367-0.0052-0.0135-0.055-0.01130.0045-0.029-0.0051-0.029515.2928144.581355.943
31.0398-0.2438-0.07080.83440.22190.67030.0096-0.2440.04740.17110.00010.05970.0275-0.1014-0.0096-0.018-0.10170.01090.04250.06820.00133.1019148.962386.072
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 329
2X-RAY DIFFRACTION2{ B|* }B3 - 329
3X-RAY DIFFRACTION3CHAIN A 401-406 AND CHAIN B 401-406A401 - 406

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