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- PDB-9s8j: Structure of protein kinase CK2alpha mutant R191Q associated with... -

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Basic information

Entry
Database: PDB / ID: 9s8j
TitleStructure of protein kinase CK2alpha mutant R191Q associated with the Okur-Chung Neurodevelopmental Syndrome
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / Protein kinase CK2 / CK2 / casein kinase II / kinase / Okur-Chung neurodevelopmental syndrome
Function / homology
Function and homology information


Phosphorylation and nuclear translocation of BMAL1 (ARNTL) and CLOCK / positive regulation of aggrephagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Phosphorylation and nuclear translocation of the CRY:PER:kinase complex / Regulation of CDH1 posttranslational processing and trafficking to plasma membrane / Receptor Mediated Mitophagy ...Phosphorylation and nuclear translocation of BMAL1 (ARNTL) and CLOCK / positive regulation of aggrephagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Phosphorylation and nuclear translocation of the CRY:PER:kinase complex / Regulation of CDH1 posttranslational processing and trafficking to plasma membrane / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / negative regulation of apoptotic signaling pathway / negative regulation of signal transduction by p53 class mediator / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of double-strand break repair via homologous recombination / positive regulation of Wnt signaling pathway / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Wnt signaling pathway / Hsp90 protein binding / peptidyl-serine phosphorylation / PML body / SPOP-mediated proteasomal degradation of PD-L1(CD274) / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / kinase activity / double-strand break repair / KEAP1-NFE2L2 pathway / rhythmic process / positive regulation of cell growth / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / protein folding / heterochromatin formation / Regulation of TP53 Activity through Phosphorylation / regulation of cell cycle / non-specific serine/threonine protein kinase / protein stabilization / negative regulation of translation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / DNA damage response / positive regulation of DNA-templated transcription / chromatin / signal transduction / DNA-templated transcription / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsWerner, C. / Gast, A. / Meyer, S.C. / Jose, J. / Niefind, K.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/11-1 Germany
German Research Foundation (DFG)NI 643/4-1 Germany
CitationJournal: To Be Published
Title: Investigation of the structure-dysfunction relationship of various OCNDS-related CK2alpha mutants
Authors: Werner, C. / Gast, A. / Caefer, D. / Fellhoefer, J. / Meyer, S.C. / Jordan, S. / Buchwald, L.M. / Than, T.L. / Schwartz, D. / Jose, J. / Niefind, K.
History
DepositionAug 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release

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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)96,38814
Polymers94,7022
Non-polymers1,68612
Water4,630257
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1947
Polymers47,3511
Non-polymers8436
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1947
Polymers47,3511
Non-polymers8436
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.280, 128.280, 125.588
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 2 through 13 or resid 15 through 258 or resid 260 through 329 or resid 401))
d_2ens_1(chain "B" and (resid 2 through 13 or resid 15 through 258 or resid 260 through 329 or resid 401))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERTHRTHRAA2 - 1322 - 33
d_12VALVALILEILEAA15 - 25835 - 278
d_13LYSLYSLYSLYSAA260 - 329280 - 349
d_14ANPANPANPANPAC401
d_21SERSERTHRTHRBB2 - 1322 - 33
d_22VALVALILEILEBB15 - 25835 - 278
d_23LYSLYSLYSLYSBB260 - 329280 - 349
d_24ANPANPANPANPBI401

NCS oper: (Code: givenMatrix: (0.00672020953114, -0.999976928984, -0.000990093161043), (0.997898226331, 0.00664241765458, 0.0644593528748), (-0.0644512891197, -0.00142119256687, 0.997919842243)Vector: ...NCS oper: (Code: given
Matrix: (0.00672020953114, -0.999976928984, -0.000990093161043), (0.997898226331, 0.00664241765458, 0.0644593528748), (-0.0644512891197, -0.00142119256687, 0.997919842243)
Vector: 62.8882221162, -62.6955937516, 32.4857061159)

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Components

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


Mass: 47350.852 Da / Num. of mol.: 2 / Mutation: R191Q
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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.73 Å3/Da / Density % sol: 54.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir: 200 mM Li2SO4, 100 mM Bis-Tris/HCl, pH 6.5, 25 % PEG3350 Protein: 5 mg per mL in 500 mM NaCl, 25 mM Tris/HCl, pH 8.5 Drop: 2 parts protein mixed with 1 part reservoir Soaking with AMPPNP/MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.438→90.708 Å / Num. obs: 28669 / % possible obs: 76.3 % / Redundancy: 8.8 % / Biso Wilson estimate: 19.78 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.361 / Net I/σ(I): 6
Reflection shellResolution: 2.438→2.722 Å / Rmerge(I) obs: 1.958 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1433 / CC1/2: 0.461

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Processing

Software
NameVersionClassification
autoPROCdata processing
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→64.14 Å / SU ML: 0.2434 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.9775
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2543 2005 7 %
Rwork0.2114 26644 -
obs0.2144 28649 76.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.62 Å2
Refinement stepCycle: LAST / Resolution: 2.48→64.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5546 0 96 257 5899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00225813
X-RAY DIFFRACTIONf_angle_d0.51287886
X-RAY DIFFRACTIONf_chiral_restr0.0431816
X-RAY DIFFRACTIONf_plane_restr0.00381002
X-RAY DIFFRACTIONf_dihedral_angle_d12.93162184
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.756481292814 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.540.327250.440364X-RAY DIFFRACTION2.65
2.55-2.610.4059160.3024260X-RAY DIFFRACTION10.51
2.61-2.690.3271460.2901599X-RAY DIFFRACTION24.45
2.69-2.780.3424980.27131283X-RAY DIFFRACTION52.75
2.78-2.880.32071390.24821885X-RAY DIFFRACTION76.41
2.88-2.990.27831770.24912368X-RAY DIFFRACTION95.46
2.99-3.130.26831880.2552466X-RAY DIFFRACTION99.62
3.13-3.290.27051870.25212475X-RAY DIFFRACTION99.96
3.29-3.50.27671910.25432463X-RAY DIFFRACTION99.92
3.5-3.770.24161870.19672498X-RAY DIFFRACTION99.96
3.77-4.150.24021820.18212516X-RAY DIFFRACTION100
4.15-4.750.22311920.15522524X-RAY DIFFRACTION100
4.75-5.980.21931870.18162567X-RAY DIFFRACTION99.96
5.99-64.140.25362100.22342676X-RAY DIFFRACTION99.55

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