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- PDB-9s76: Structure of protein kinase CK2alpha mutant Y50C associated with ... -

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Basic information

Entry
Database: PDB / ID: 9s76
TitleStructure of protein kinase CK2alpha mutant Y50C associated with the Okur-Chung Neurodevelopmental Syndrome
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / Okur-Chung neurodevelopmental syndrome / OCNDS / CK2 / protein kinase CK2 / casein kinase II
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: 1.73 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: Structure of protein kinase CK2alpha mutant Y50C associated with the Okur-Chung Neurodevelopmental Syndrome
Authors: Werner, C. / Gast, A. / Caefer, D. / Fellhoefer, J. / Jordan, S. / Meyer, S.C. / Buchwald, L.M. / 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)96,51816
Polymers94,6402
Non-polymers1,87814
Water7,584421
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,45110
Polymers47,3201
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)48,0676
Polymers47,3201
Non-polymers7475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.662, 127.662, 124.532
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: (0.00711123167106, -0.997623785499, 0.0685289208393), (0.99997471244, 0.0070897328256, -0.000556929034435), (6.97539120104E-5, 0.0685311483614, 0.997648974759)Vector: - ...NCS oper: (Code: given
Matrix: (0.00711123167106, -0.997623785499, 0.0685289208393), (0.99997471244, 0.0070897328256, -0.000556929034435), (6.97539120104E-5, 0.0685311483614, 0.997648974759)
Vector: -64.4035322557, -62.433041066, 32.4766917287)

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Components

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


Mass: 47319.887 Da / Num. of mol.: 2 / Mutation: Y50C
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: isolated from a natural source / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir: Index (Hampton) G3, 200 mM lithium sulphate, 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 supplemented with DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.726→90.271 Å / Num. obs: 76585 / % possible obs: 70.9 % / Redundancy: 26.4 % / Biso Wilson estimate: 27.29 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.142 / Net I/σ(I): 14.5
Reflection shellResolution: 1.726→1.902 Å / Rmerge(I) obs: 2.605 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3829 / CC1/2: 0.434

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
autoPROCdata processing
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→56.8 Å / SU ML: 0.2012 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9093
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.226 1996 2.61 %
Rwork0.1852 74373 -
obs0.1863 76369 70.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.29 Å2
Refinement stepCycle: LAST / Resolution: 1.73→56.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5569 0 106 421 6096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115847
X-RAY DIFFRACTIONf_angle_d1.1957933
X-RAY DIFFRACTIONf_chiral_restr0.0706821
X-RAY DIFFRACTIONf_plane_restr0.01161009
X-RAY DIFFRACTIONf_dihedral_angle_d15.32712197
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.647622184867 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.770.273350.33158X-RAY DIFFRACTION2.15
1.77-1.820.4041160.295609X-RAY DIFFRACTION8.29
1.82-1.870.355400.28171530X-RAY DIFFRACTION20.63
1.87-1.930.3469710.28362702X-RAY DIFFRACTION36.32
1.93-20.27391120.26084272X-RAY DIFFRACTION57.44
2-2.080.28171550.24535784X-RAY DIFFRACTION77.61
2.08-2.170.28331960.22527450X-RAY DIFFRACTION99.64
2.17-2.290.26241990.21467206X-RAY DIFFRACTION96.66
2.29-2.430.23461930.19367481X-RAY DIFFRACTION100
2.43-2.620.2442030.19447516X-RAY DIFFRACTION100
2.62-2.880.22581960.19646852X-RAY DIFFRACTION91.19
2.88-3.30.22181980.17447584X-RAY DIFFRACTION100
3.3-4.160.19571970.15617311X-RAY DIFFRACTION95.51
4.16-56.80.20442150.16917918X-RAY DIFFRACTION99.58
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)
10.4327469805140.109637817654-0.1798773024551.12020326138-0.1322605476051.502192881290.1689487601190.11873473195-0.0963652042675-0.258010781629-0.08915364025860.01314591138070.06291674518110.1397356481930.0001017426635250.2166663601720.04412287737810.00855519623350.190121192559-0.003963681015050.167693087106-3.25205879545-47.043813419910.0665518737
20.456940256785-0.4740546888690.2668044016450.7874316430910.09635363781330.6110812780160.0143456446-0.6536114653580.228979830157-0.0438932572316-0.2912575240510.1764396508170.05538664015390.0850350733591-0.004939000897610.21332392863-0.05106853664680.01328227966880.4467215217150.05519398825880.2669721862729.11099704561-50.456933017324.8081754388
31.937680337960.04323235972430.2269571023960.8247063226250.1035614709830.401732959726-0.0791055889653-0.430577520970.06513317260580.2198607246710.0649102073675-0.190016357480.03634866782420.0762352764842-0.01018489085330.219539579130.059875098573-0.01359868802510.270430136153-0.007522393004940.2155278695320.205339626391-40.743166753522.1869247584
41.45516425533-1.18409725087-0.2758962532361.47284213242-0.5298100626521.68212499246-0.077901461594-0.358187380485-0.02515003868350.03209294920170.09253418585720.01067165518310.00562882397968-0.05514046358730.002254671768990.1080728982840.05742836579590.004202126732110.2167943737450.005688275458990.150406552776-11.6838777339-42.58979295322.3690082133
52.29260069473-1.035598986191.557689907080.685698361103-0.08051829510872.89127650307-0.0830383961474-0.56960667349-0.6024581336040.3122687618520.4416689080490.4333138942750.264049449261-0.5403012626421.554409183770.2081753168120.08827404057530.08319620783910.5502023670220.1701818375810.388115804796-28.4699038487-44.419093382730.7900210983
60.635755704506-0.135433924257-0.4496025546790.1805173241230.3221391247251.74365213892-0.0344433004392-0.4094333221480.2750623707250.1929590553290.186307953194-0.0679748547295-0.325906746184-0.133263463371-0.01816685123440.2203329321420.250986474726-0.01383388458640.381643383652-0.08692267209380.250537789119-17.9212251846-28.05892184827.3803262309
70.760070357841-0.5939797900430.318896710473.76023922397-0.5857065287060.5292044030740.05692365148240.210113075722-0.185791177214-0.6111421310040.0591918567321-0.1571431177940.385975569585-0.119160817564-0.07754191547980.287350766621-0.0918797655266-0.009805335653080.253654607586-0.0660056381780.22709949367-21.8618420546-78.040855801134.5341426192
80.3490654326520.09878820282620.07673720450120.05951620128830.107651219410.238241695432-0.1859740440330.1696048367670.0866607793847-0.242201824110.0979920743307-0.262802181627-0.5205081280090.208685197491-0.002067532672590.393935758807-0.03131380063830.02091401835810.270947290479-0.02215524472260.270226340099-11.2926084107-52.689160293244.5146504808
90.8739569770420.5756118052250.03427938650250.4900084432960.2673511566780.813815665386-0.116135257041-0.04675944366810.0489730752830.267627725864-0.107050322227-0.01929722534440.06636225052610.04219856198041.26184792134E-50.3037407587130.04265322364-0.01116906903530.242676394719-0.01414507427290.272719085576-12.4006018613-53.934414917353.7390681986
100.061720515584-0.02870357370790.02291077888360.606485056298-0.2321410322120.448078616603-0.09160652369290.08185165987030.0194332353037-0.113933020925-0.0187549702394-0.17920277905-0.1349213039230.0828060855224-0.0001920529164330.162397268044-0.03652513878940.02886208437310.235293554422-0.02406056633550.244523803417-14.367807915-59.117072555144.0711219684
110.185569289020.271746479463-0.4927351226791.08825187262-0.6392023033691.315222621220.250973974111-0.7399260093340.05968129124390.623257370567-0.4135100968650.1713520184030.01641275909980.0911894602611-0.5151383046910.429588098787-0.1100715048380.06424510959750.48018925732-0.05944881710180.240238092596-23.0399703478-60.888278217261.5555272196
120.5400744033670.34554312042-0.1993868713830.742567317289-0.5599863744780.4312913957830.0835765914302-0.1580801339940.1123274745540.256949543696-0.01130650702480.272918345965-0.215401568376-0.3052752794480.0004673456715330.182057813578-0.03193413302440.03406514334520.293336958229-0.0473859309980.225266227962-28.4990369105-68.134232817754.2273836399
131.094820599470.9982111427310.2642092354651.4072139725-0.4904466556841.1652930710.110721645703-0.0721183265425-0.1076362003290.0856328503799-0.0371248156623-0.108477323750.116839148688-0.0228449055380.0002613812142770.166497801969-0.0502228157268-0.01326098244850.241228134398-0.02191036323290.218197513669-19.4878718378-76.957207635350.9385353052
140.760541038838-0.135017302951-0.3595491225210.8182210523580.2231553999690.2683895669950.0902837765951-0.8152930063690.01112923130180.5466939459380.0618489874849-0.3570331919830.07714305366840.2917094195650.04157806309780.308872661759-0.0877061717488-0.09164867901480.4358070149210.02333087764250.274650589998-17.120191439-84.178356490364.5316113138
151.987228469391.51232047481-1.346640972281.67615153743-0.2018155137922.217150949170.0065190790935-0.537496377202-0.9563646246610.175461120173-0.0780995687491-0.8548226333440.7818336873850.522780603717-0.1180792924930.3876956166230.0020270494934-0.1325769202990.3658636775420.09095974479820.575712504258-17.0925534794-96.176503001855.9676804589
161.144379354150.04513069872640.2430807421530.7809053210430.2820862726790.1475341738880.164585547098-0.474517601069-0.1140066995730.293195217695-0.08041875064910.1430553373760.18783050257-0.2224734162760.5429060201590.24574051004-0.187970728797-0.01667335900890.3755040390380.03101016270920.20191447825-31.5173388527-83.959461634161.5202898675
171.404612486840.648216665523-0.8730382533611.953727793910.7385750721012.767788102120.06173155512520.212357955590.334164262010.01446382492620.006407137204450.6880097796840.0750825187313-0.7007250656920.2303635058950.141099977495-0.1289653891880.02177840931740.4708542447780.0256671005150.36837113355-40.2710459329-75.163317405453.1966054722
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 44 )AA2 - 441 - 43
22chain 'A' and (resid 45 through 74 )AA45 - 7444 - 73
33chain 'A' and (resid 75 through 149 )AA75 - 14974 - 148
44chain 'A' and (resid 150 through 227 )AA150 - 227149 - 226
55chain 'A' and (resid 228 through 284 )AA228 - 284227 - 283
66chain 'A' and (resid 285 through 329 )AA285 - 329284 - 328
77chain 'B' and (resid 2 through 24 )BC2 - 241 - 23
88chain 'B' and (resid 25 through 44 )BC25 - 4424 - 43
99chain 'B' and (resid 45 through 74 )BC45 - 7444 - 73
1010chain 'B' and (resid 75 through 108 )BC75 - 10874 - 107
1111chain 'B' and (resid 109 through 129 )BC109 - 129108 - 128
1212chain 'B' and (resid 130 through 168 )BC130 - 168129 - 167
1313chain 'B' and (resid 169 through 227 )BC169 - 227168 - 226
1414chain 'B' and (resid 228 through 249 )BC228 - 249227 - 248
1515chain 'B' and (resid 250 through 280 )BC250 - 280249 - 279
1616chain 'B' and (resid 281 through 314 )BC281 - 314280 - 313
1717chain 'B' and (resid 315 through 329 )BC315 - 329314 - 328

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