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- PDB-9s7i: Structure of protein kinase CK2alpha mutant D175G associated with... -

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Basic information

Entry
Database: PDB / ID: 9s7i
TitleStructure of protein kinase CK2alpha mutant D175G associated with the Okur-Chung Neurodevelopmental Syndrome
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / Protein kinase / CK2 / casein kinase II / OCNDS / Okur-Chung neurodevelopmental syndorme
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: 2.11 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. / Jordan, S. / Meyer, S.C. / 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)96,87117
Polymers94,6442
Non-polymers2,22715
Water3,477193
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2126
Polymers47,3221
Non-polymers8905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,65911
Polymers47,3221
Non-polymers1,33710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.812, 128.812, 125.320
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 227 or resid 229...
d_2ens_1(chain "B" and (resid 2 through 227 or resid 229...

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_11SERSERPHEPHEAA2 - 22722 - 247
d_12LYSLYSILEILEAA229 - 258249 - 278
d_13LYSLYSGLNGLNAA260 - 310280 - 330
d_14ARGARGALAALAAA312 - 332332 - 352
d_15ANPANPANPANPAC401
d_21SERSERPHEPHEBB2 - 22722 - 247
d_22LYSLYSILEILEBB229 - 258249 - 278
d_23LYSLYSGLNGLNBB260 - 310280 - 330
d_24ARGARGALAALABB312 - 332332 - 352
d_25ANPANPANPANPBH401

NCS oper: (Code: givenMatrix: (0.00758439944766, -0.99996661426, 0.00304092924189), (0.998597638439, 0.00773328477547, 0.0523732069887), (-0.0523949748422, 0.00263944543746, 0.998622951839)Vector: 63. ...NCS oper: (Code: given
Matrix: (0.00758439944766, -0.99996661426, 0.00304092924189), (0.998597638439, 0.00773328477547, 0.0523732069887), (-0.0523949748422, 0.00263944543746, 0.998622951839)
Vector: 63.3198914242, -63.2732099472, 31.7110223034)

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Components

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


Mass: 47321.879 Da / Num. of mol.: 2 / Mutation: D175G
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-SO4 / SULFATE ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM Li2SO4, 100 mM Bis-Tris/HCl, pH 6.5, 25 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 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: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.11→91.08 Å / Num. obs: 50386 / % possible obs: 82.8 % / Redundancy: 18 % / Biso Wilson estimate: 47.16 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.229 / Net I/σ(I): 12.7
Reflection shellResolution: 2.11→2.284 Å / Rmerge(I) obs: 4.259 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2519 / CC1/2: 0.546

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→91.08 Å / SU ML: 0.2332 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.8715
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2552 2004 4.16 %
Rwork0.213 46218 -
obs0.2147 48222 79.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.1 Å2
Refinement stepCycle: LAST / Resolution: 2.11→91.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5578 0 126 193 5897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025873
X-RAY DIFFRACTIONf_angle_d0.53147966
X-RAY DIFFRACTIONf_chiral_restr0.045819
X-RAY DIFFRACTIONf_plane_restr0.00461008
X-RAY DIFFRACTIONf_dihedral_angle_d13.86142199
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.874224469764 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.170.598660.406127X-RAY DIFFRACTION3.1
2.17-2.220.4528210.3795480X-RAY DIFFRACTION11.76
2.22-2.290.323600.33381459X-RAY DIFFRACTION35.62
2.29-2.360.32441140.28882528X-RAY DIFFRACTION61.57
2.36-2.450.28391660.26493847X-RAY DIFFRACTION93.39
2.45-2.550.29311730.2654129X-RAY DIFFRACTION99.98
2.55-2.660.2921760.27064131X-RAY DIFFRACTION99.98
2.66-2.80.32861860.27514139X-RAY DIFFRACTION99.98
2.8-2.980.34731730.25694143X-RAY DIFFRACTION100
2.98-3.210.26791810.21654182X-RAY DIFFRACTION100
3.21-3.530.25761810.21124162X-RAY DIFFRACTION99.98
3.53-4.040.23891840.18794214X-RAY DIFFRACTION100
4.04-5.090.19411850.16894245X-RAY DIFFRACTION99.98
5.09-91.080.24431980.20634432X-RAY DIFFRACTION99.31
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)
11.685741886351.313533283370.8578499239934.345501634392.054850269812.61886663037-0.1360093508290.1620478523690.0880860371395-0.1118582939810.184822810917-0.0809090379408-0.2967842482280.068872842896-0.08019397415510.28878436421-0.007383201351260.02416091505680.2747037446180.0610533267350.25524744335749.40763599371.03718810386-15.4204917236
22.600581474040.751182787414-1.288559938213.87055338382-0.3695628582172.587044864710.33175787127-0.6705672575730.08047036106030.664470430799-0.346582079233-0.352633561202-0.3233713805830.3475263845940.08067739998140.402733560639-0.0582928865228-0.03291739673670.3789062219760.02111216650090.32310816518744.15174140644.21582379131-5.54476735565
31.98640100770.637154054834-0.1237848421222.10522972761-0.4051993743922.342159663120.116388854479-0.154629688114-0.1657661358020.158064741721-0.140932004475-0.06991905789820.152904407680.04806134267920.02424734897010.285110529443-0.07437614345260.005989333109430.2507590956350.04923014007850.28307415425239.1281803043-17.6336277856-4.68501386524
45.613076764320.3767301134360.7820116688023.661797883530.7716557858333.21332713384-0.02522692832960.884076819422-0.163758166702-0.6221434449240.0605634184843-0.05940656500540.02190890858440.322083721091-0.01349985392020.3328016245940.07413332377710.06618071510250.362964574121-0.0155457267030.26331671250378.8528623698-21.59187057993.69416538908
53.5568518493-0.79857697733-2.031611777183.107790100910.3050302140864.027830344770.03977689053110.1828531355880.0955691981776-0.0542025626705-0.1435284139220.0663988749192-0.11360002353-0.2673489631020.08845060768650.1756131374720.0224652456517-0.04219548372330.2613440783670.02100511459540.20520196608156.7033530839-12.948621288617.0360117214
62.93553670405-1.838116799571.518578187232.17032963977-1.482018072861.06099559514-0.368871153806-0.705698489673-0.3918556951870.5102674660460.347542256910.304563979378-0.162031306981-0.2948751495880.02424941646410.4575431731410.08564874363190.06053313460970.4342497391920.08007653575760.36942927069166.7135287069-28.231465826.8865484509
72.54301249008-0.5338115748990.5392466413522.58021551131-0.730477140852.5733470368-0.196207862923-0.2996288231970.2080769374780.4466230376260.128561249638-0.106365562244-0.247337034776-0.02528698707650.06526771842710.3245409710130.110362993098-0.01738093742660.267425947127-0.03597366690690.3012854489177.7983431933-19.868650384324.097394093
82.72232380256-0.496773501108-0.005615051911452.36379063896-0.6934523342182.36248172803-0.159515149347-0.273527854563-0.06607619288520.4179455439440.0708773164231-0.3933561256160.02253637960690.1657678438050.1321153046530.2674616327070.126671360504-0.06268353081060.3030791817330.01050469099190.27046351043687.7713062198-27.940064178426.7160288706
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 87 )AA2 - 871 - 86
22chain 'A' and (resid 88 through 129 )AA88 - 12987 - 128
33chain 'A' and (resid 130 through 332 )AA130 - 332129 - 331
44chain 'B' and (resid 2 through 24 )BC2 - 241 - 23
55chain 'B' and (resid 25 through 108 )BC25 - 10824 - 107
66chain 'B' and (resid 109 through 149 )BC109 - 149108 - 148
77chain 'B' and (resid 150 through 249 )BC150 - 249149 - 248
88chain 'B' and (resid 250 through 332 )BC250 - 332249 - 331

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