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- PDB-9s7h: Structure of protein kinase CK2alpha mutant H160R associated with... -

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Basic information

Entry
Database: PDB / ID: 9s7h
TitleStructure of protein kinase CK2alpha mutant H160R associated with the Okur-Chung Neurodevelopmental Syndrome
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / Protein kinase CK2 / CK2 / casein kinase II / EPK / CSNK2A1 / OCNDS / 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: 2.09 Å
AuthorsWerner, C. / Gast, A. / Jose, J. / Niefind, K.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/4-1 Germany
German Research Foundation (DFG)NI 643/11-1 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. / Than, T.L. / Schwartz, D. / Jose, J. / Niefind, K.
History
DepositionAug 4, 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)97,06020
Polymers94,7982
Non-polymers2,26218
Water4,035224
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,53010
Polymers47,3991
Non-polymers1,1319
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,53010
Polymers47,3991
Non-polymers1,1319
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.712, 128.712, 124.790
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 258 or resid 260...
d_2ens_1(chain "B" and (resid 2 through 258 or resid 260 through 310 or resid 312 through 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_11SERSERILEILEAA2 - 25822 - 278
d_12LYSLYSGLNGLNAA260 - 310280 - 330
d_13ARGARGGLNGLNAA312 - 331332 - 351
d_14ANPANPANPANPAC401
d_21SERSERILEILEBB2 - 25822 - 278
d_22LYSLYSGLNGLNBB260 - 310280 - 330
d_23ARGARGGLNGLNBB312 - 331332 - 351
d_24ANPANPANPANPBL401

NCS oper: (Code: givenMatrix: (0.00748322869651, 0.9999651559, 0.0036997667105), (-0.998622915805, 0.00728095819952, 0.0519543999682), (0.0519256518172, -0.00408345847699, 0.998642604764)Vector: 63. ...NCS oper: (Code: given
Matrix: (0.00748322869651, 0.9999651559, 0.0036997667105), (-0.998622915805, 0.00728095819952, 0.0519543999682), (0.0519256518172, -0.00408345847699, 0.998642604764)
Vector: 63.5405684847, -65.894037602, -28.6040177129)

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Components

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


Mass: 47398.965 Da / Num. of mol.: 2 / Mutation: H160R
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 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 54.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM Li2SO4, 100 mM Bis-tris/HCl, pH 6.5, 25 % PEG 3350 Protein 5 mg per mL in 500 mM NaCl, 25 mM TRIS/HCl, pH 8.5 2 parts protein mixed with one 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: ID30B / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.088→91.013 Å / Num. obs: 40809 / % possible obs: 65.2 % / Redundancy: 11.2 % / Biso Wilson estimate: 32.62 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.388 / Net I/σ(I): 9.1
Reflection shellResolution: 2.088→2.39 Å / Rmerge(I) obs: 4.137 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2040 / CC1/2: 0.386

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Processing

Software
NameVersionClassification
autoPROCdata processing
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→91.01 Å / SU ML: 0.2274 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2324
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2374 2037 4.99 %
Rwork0.187 38744 -
obs0.1896 40781 65.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.41 Å2
Refinement stepCycle: LAST / Resolution: 2.09→91.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5583 0 126 224 5933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045861
X-RAY DIFFRACTIONf_angle_d0.70967950
X-RAY DIFFRACTIONf_chiral_restr0.0477819
X-RAY DIFFRACTIONf_plane_restr0.00611006
X-RAY DIFFRACTIONf_dihedral_angle_d13.97412200
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.763228293165 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.140.479520.275649X-RAY DIFFRACTION1.26
2.14-2.190.415660.2909140X-RAY DIFFRACTION3.57
2.19-2.250.3182180.3156261X-RAY DIFFRACTION6.85
2.25-2.320.3085280.2769486X-RAY DIFFRACTION12.61
2.32-2.390.2964410.28971009X-RAY DIFFRACTION25.49
2.39-2.480.3858790.27271821X-RAY DIFFRACTION45.95
2.48-2.570.31751820.27233055X-RAY DIFFRACTION78.21
2.57-2.690.32181760.25193787X-RAY DIFFRACTION96.19
2.69-2.830.25511700.23713986X-RAY DIFFRACTION100
2.83-3.010.23982330.21383923X-RAY DIFFRACTION100
3.01-3.240.24392310.19173949X-RAY DIFFRACTION100
3.24-3.570.23022000.17574003X-RAY DIFFRACTION100
3.57-4.090.20942180.1534000X-RAY DIFFRACTION100
4.09-5.150.19062160.13834065X-RAY DIFFRACTION99.98
5.15-91.010.23992370.18224210X-RAY DIFFRACTION99.44
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)
11.945199884960.13116007929-0.1688406957043.604423120330.210352571441.26047081-0.04034575358850.354464466806-0.0190429267162-0.6625976068310.1317331282910.2258083199730.312950813397-0.1222077297340.009805743102650.214868824238-0.0785571653925-0.03225852483690.221757434966-0.03806267964020.102663390352-21.6233371641-78.899396544534.813854638
21.70234358817-0.637270306833-0.2504172559373.378588662173.071125233745.67174025639-0.147222285757-0.07991562231160.05377322602010.09262533718840.0111052826622-0.198909715226-0.1805677026410.09444484373020.03085816931980.166667981682-0.01537711872430.03614530471310.1948951615290.0167453640820.125164801519-11.4494569664-54.920080520749.8740563288
32.269781202751.104976549150.780298539492.991819402460.8598801797582.0053909804-0.1729282855060.1471270319340.0105350472945-0.2800819102260.0196528199362-0.005210452233-0.095784292120.06117308612050.1238428469710.149977702205-0.03308295156910.03448735624570.1295570127530.003377016341070.149344383461-14.0883461381-57.82353838146.7467162777
40.008125437046170.0266660470162-0.04384336777210.129573266412-0.1928902696950.2760895795780.0346183535478-0.2728169751260.1629401055640.355155706564-0.1026230850810.26433416344-0.07221986218870.00357378542966-0.01814894705670.316137181092-0.08233638234220.09607098755190.334322704042-0.08299548013160.221741178743-28.2044837469-66.53910496857.9157324477
51.430297232480.347173859841-0.03846871623742.09896088910.03089957055511.602303638920.15922833197-0.323756887878-0.1114026456030.275894217524-0.163720762822-0.1211777753350.03995520580480.145859257262-0.02193861174270.19821675192-0.0942070526618-0.02747198205860.229540108813-0.0005488097989140.15351287866-19.7493638267-77.635919177155.0164990392
61.903014912760.563433045047-0.6956725176030.6393072996020.09216591968963.385822685370.0264597779473-0.347754487337-0.7293521365530.288632033827-0.107421033304-0.5892540017220.7682495255430.4019017470460.08043194953330.3721070481130.00455786787882-0.1170178779550.2643969745740.1070452042130.509031081294-17.1885129138-97.092576090456.3338287346
70.392919366666-0.313355504506-0.3666183646620.2737410650280.2629575933790.4314190239340.156900301103-0.4614635825250.0268371085250.385313031482-0.1244413500570.135315619593-0.009090462656040.05160829726510.4894167632170.329916912263-0.2062976185940.06540486271490.415142597414-0.02579376365760.139558452018-31.6766376832-85.120381170561.5778895039
85.823530645881.28375057619-1.896594815674.369976543751.241796836846.141642218030.418160662629-0.1281826440220.5037974076160.127875952707-0.1833112814670.522603294131-0.342169435923-0.666041776346-0.1613159403990.23638268916-0.1028879982770.05268214836420.322420838531-0.03819060527480.285449858144-40.6763560441-75.103300216553.5161278889
93.15741636722-0.9667772352251.141576308481.13632506795-0.5622828910381.91930624760.08050061103520.0205083302912-0.0248344348491-0.184882178096-0.0868360834892-0.0990814389413-0.001504444645920.296191532366-0.0469092470780.195699559580.006936449761570.05606206394050.231262398876-0.02053996862110.1540508292611.00231934372-49.281555803315.6938447872
101.55342909730.587715986242-0.1946409426641.462676514141.324277370683.13915987264-0.195083049015-0.262883906761-0.1277825805790.5899473526390.221776979977-0.2754780851190.4250816186470.1646230068360.03636259774740.3151092747250.0759582328407-0.01500091484030.3435710575430.0004348739065260.1808796336574.4454124342-44.063672182725.1679710532
111.43378765734-0.652454554487-0.3976453709111.01018183986-0.1155247494921.73612327673-0.107768291709-0.25415812166-0.01252024515640.1111855096690.216409028490.178331117361-0.071372131938-0.274802352474-0.04493364433550.1157261498490.1188747186230.04185807646940.2332852826220.003673326283970.104543783432-17.5717645554-39.093081560926.4749153544
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 24 )AA2 - 241 - 23
22chain 'A' and (resid 25 through 58 )AA25 - 5824 - 57
33chain 'A' and (resid 59 through 108 )AA59 - 10858 - 107
44chain 'A' and (resid 109 through 149 )AA109 - 149108 - 148
55chain 'A' and (resid 150 through 249 )AA150 - 249149 - 248
66chain 'A' and (resid 250 through 280 )AA250 - 280249 - 279
77chain 'A' and (resid 281 through 314 )AA281 - 314280 - 313
88chain 'A' and (resid 315 through 331 )AA315 - 331314 - 330
99chain 'B' and (resid 2 through 87 )BC2 - 871 - 86
1010chain 'B' and (resid 88 through 129 )BC88 - 12987 - 128
1111chain 'B' and (resid 130 through 331 )BC130 - 331129 - 330

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