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- PDB-9epy: Crystal structure of human Casein Kinase II subunit alpha (CK2a1)... -

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Basic information

Entry
Database: PDB / ID: 9epy
TitleCrystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with allosteric ligand FGC3330
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / CK2 / Kinase / Chemical / allosteric Inhibitor
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 signal transduction by p53 class mediator / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / : / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / PML body / Regulation of PTEN stability and activity / Wnt signaling pathway / positive regulation of protein catabolic process / KEAP1-NFE2L2 pathway / kinase activity / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / DNA damage response / 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. / 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
Similarity search - Domain/homology
: / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKraemer, A. / Greco, F. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
Citation
Journal: Eur.J.Med.Chem. / Year: 2024
Title: Synthesis and evaluation of chemical linchpins for highly selective CK2 alpha targeting.
Authors: Greco, F.A. / Kramer, A. / Wahl, L. / Elson, L. / Ehret, T.A.L. / Gerninghaus, J. / Mockel, J. / Muller, S. / Hanke, T. / Knapp, S.
#1: Journal: Biorxiv / Year: 2024
Title: Synthesis and evaluation of chemical linchpins for highly selective CK2 alpha targeting
Authors: Greco, F.A. / Kramer, A. / Wahl, L. / Elson, L. / Ehret, T.A.L. / Gerninghaus, J. / Mockel, J. / Muller, S. / Hanke, T. / Knapp, S.
History
DepositionMar 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Database references / Category: citation / citation_author
Revision 1.2Aug 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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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)83,51723
Polymers80,6562
Non-polymers2,86221
Water36020
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,80712
Polymers40,3281
Non-polymers1,47911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,71111
Polymers40,3281
Non-polymers1,38310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.645, 126.645, 124.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 40327.977 Da / Num. of mol.: 2
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


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-A1H6G / ~{N}-[(3-chloranyl-4-phenyl-phenyl)methyl]-7-[(2-methyl-1,3-benzothiazol-6-yl)sulfonyl]-7-azaspiro[3.5]nonan-2-amine


Mass: 552.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H30ClN3O2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.09 Å3/Da / Density % sol: 60.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M bis-tris pH 5.5 23-26% (v/v) PEG 3350 0.2 M ammonia sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.65→44.82 Å / Num. obs: 30001 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 0.998 / Net I/σ(I): 10.2
Reflection shellResolution: 2.65→2.78 Å / Num. unique obs: 3904 / CC1/2: 0.761
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→44.82 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.916 / SU B: 31.39 / SU ML: 0.295 / Cross valid method: THROUGHOUT / ESU R: 0.572 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26864 1480 4.9 %RANDOM
Rwork0.22642 ---
obs0.22848 28464 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.729 Å2
Baniso -1Baniso -2Baniso -3
1-3.99 Å2-0 Å20 Å2
2--3.99 Å2-0 Å2
3----7.98 Å2
Refinement stepCycle: 1 / Resolution: 2.65→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5343 0 167 20 5530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125654
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165069
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.6697699
X-RAY DIFFRACTIONr_angle_other_deg0.551.60811605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.855656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.976540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.07510889
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2814
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026714
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021360
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7625.42630
X-RAY DIFFRACTIONr_mcbond_other3.7595.42630
X-RAY DIFFRACTIONr_mcangle_it5.6419.7263284
X-RAY DIFFRACTIONr_mcangle_other5.649.7263285
X-RAY DIFFRACTIONr_scbond_it4.5065.8833024
X-RAY DIFFRACTIONr_scbond_other4.4695.8683017
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.65310.6474400
X-RAY DIFFRACTIONr_long_range_B_refined8.61773.8611475
X-RAY DIFFRACTIONr_long_range_B_other8.61773.8611476
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 119 -
Rwork0.37 2047 -
obs--100 %
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)
10.9628-0.9566-0.01523.82450.07481.93740.07180.0283-0.0325-0.5059-0.05010.0296-0.0698-0.179-0.02170.07560.01650.01370.02950.02890.129241.563810.077139.4154
23.6301-1.19960.32111.09420.00152.0378-0.1018-0.36640.12450.31780.1097-0.02160.2235-0.0013-0.00790.16080.01510.00640.0399-0.020.11588.875442.35920.9329
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 330
2X-RAY DIFFRACTION2B3 - 331

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