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- PDB-5ku8: Crystal structure of CK2 -

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Basic information

Entry
Database: PDB / ID: 5ku8
TitleCrystal structure of CK2
ComponentsCasein kinase II subunit alphaCasein kinase 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase / CK2 / inhibitor / 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 / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / peptidyl-threonine phosphorylation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of protein catabolic process / rhythmic process / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / protein stabilization / regulation of cell cycle / non-specific serine/threonine protein kinase / 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-6XK / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsFerguson, A.D. / Dowling, J.
CitationJournal: Not Published
Title: Crystal structure of CK2
Authors: Ferguson, A.D.
History
DepositionJul 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_abbrev / _citation.journal_id_CSD
Revision 1.2Oct 4, 2023Group: 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)82,84243
Polymers79,1802
Non-polymers3,66241
Water4,360242
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,76826
Polymers39,5901
Non-polymers2,17825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,07417
Polymers39,5901
Non-polymers1,48316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.914, 125.914, 124.617
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Casein kinase II subunit alpha / Casein kinase 2 / CK II alpha


Mass: 39590.105 Da / Num. of mol.: 2 / Fragment: UNP residues 2-332
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-6XK / ~{N}-[2-[(1~{S},2~{S})-2-(aminomethyl)cyclopropyl]-5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]phenyl]ethanamide


Mass: 416.479 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H24N8O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 3.12 Å3/Da / Density % sol: 60.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 22-26% PEG 6K, 200 mM ammonium sulfate, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.22→32.5 Å / Num. obs: 47563 / % possible obs: 94.5 % / Redundancy: 15.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.253 / Net I/σ(I): 14.6
Reflection shellResolution: 2.22→2.34 Å / Redundancy: 15.7 % / Mean I/σ(I) obs: 2.3 / CC1/2: 0.913 / % possible all: 80

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Processing

Software
NameVersionClassification
BUSTER-TNT2.11.7refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5h8b

5h8b


Resolution: 2.22→32.5 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.902 / Rfactor Rfree error: 0.01 / SU R Cruickshank DPI: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.216 / SU Rfree Blow DPI: 0.174 / SU Rfree Cruickshank DPI: 0.174
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2348 4.97 %RANDOM
Rwork0.183 ---
obs0.185 47220 94.5 %-
Displacement parametersBiso max: 123.12 Å2 / Biso mean: 35.02 Å2 / Biso min: 15.02 Å2
Baniso -1Baniso -2Baniso -3
1--6.1207 Å20 Å20 Å2
2---6.1207 Å20 Å2
3---12.2414 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 2.22→32.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5566 0 230 242 6038
Biso mean--49.28 35.83 -
Num. residues----659
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2091SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes148HARMONIC2
X-RAY DIFFRACTIONt_gen_planes878HARMONIC5
X-RAY DIFFRACTIONt_it5913HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion695SEMIHARMONIC5
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_contact6726SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5913HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7953HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion20.29
LS refinement shellResolution: 2.22→2.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 99 4.61 %
Rwork0.232 2050 -
all-2149 -
obs--59.86 %
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)
10.42-0.3344-0.24321.0559-0.17410.55260.02640.03590.0288-0.06460.00620.012-0.0438-0.0135-0.0326-0.05970.0204-0.0211-0.057-0.0223-0.1049-22.2798-53.827639.1425
21.010.3208-0.28260.5285-0.00220.7371-0.01740.0450.0443-0.0133-0.0060.0061-0.03890.02290.0234-0.0441-0.0105-0.0301-0.08840.0015-0.11267.5951-41.69929.4626
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 332
2X-RAY DIFFRACTION2{ B|* }B2 - 332

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