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- PDB-9s6g: Structure of protein kinase CK2alpha mutant R47Q associated with ... -

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Basic information

Entry
Database: PDB / ID: 9s6g
TitleStructure of protein kinase CK2alpha mutant R47Q associated with the Okur-Chung Neurodevelopmental Syndrome
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / Okur-Chung Neurodevelopmental Syndrome / OCNDS / CK2 / protein kinase / 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: 1.81 Å
AuthorsWerner, C. / Gast, A. / Buchwald, L. / 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 R47Q associated with the Okur-Chung Neurodevelopmental Syndrome
Authors: Werner, C. / Gast, A. / Caefer, D. / Fellhoefer, J. / Jordan, S. / Meyer, S.C. / Buchwald, L. / Than, T.L. / Schwartz, D. / Niefind, K.
History
DepositionAug 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 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)96,94019
Polymers94,7022
Non-polymers2,23817
Water5,549308
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4589
Polymers47,3511
Non-polymers1,1078
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,48210
Polymers47,3511
Non-polymers1,1319
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.313, 128.313, 124.765
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 117 or resid 119...
d_2ens_1(chain "B" and (resid 2 through 117 or resid 119...

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_11SERSERASNASNAA2 - 11722 - 137
d_12THRTHRILEILEAA119 - 258139 - 278
d_13LYSLYSGLNGLNAA260 - 310280 - 330
d_14ARGARGGLNGLNAA312 - 331332 - 351
d_15ANPANPANPANPAC401
d_21SERSERASNASNBB2 - 11722 - 137
d_22THRTHRILEILEBB119 - 258139 - 278
d_23LYSLYSGLNGLNBB260 - 310280 - 330
d_24ARGARGGLNGLNBB312 - 331332 - 351
d_25ANPANPANPANPBK401

NCS oper: (Code: givenMatrix: (0.00938832842824, -0.998246148079, 0.0584507239821), (0.999952084938, 0.00953431243354, 0.00221916969754), (-0.00277256506692, 0.0584270890181, 0.99828782831)Vector: - ...NCS oper: (Code: given
Matrix: (0.00938832842824, -0.998246148079, 0.0584507239821), (0.999952084938, 0.00953431243354, 0.00221916969754), (-0.00277256506692, 0.0584270890181, 0.99828782831)
Vector: -64.5300453044, -62.9006257282, 32.0568661667)

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Components

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


Mass: 47350.852 Da / Num. of mol.: 2 / Mutation: R47Q
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: isolated from a natural source / 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: isolated from a natural source / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir: 200 mM Li2SO4, 100 mM Bis-Tris HCl, pH 6.5 and 25 % PEG 3350 Protein: 5 mg per mL in 500 mM NaCl, 25 mM Tris HCl, pH 8.5 Drop: 2 to 1 mix of protein to reservoir Complex formation ...Details: Reservoir: 200 mM Li2SO4, 100 mM Bis-Tris HCl, pH 6.5 and 25 % PEG 3350 Protein: 5 mg per mL in 500 mM NaCl, 25 mM Tris HCl, pH 8.5 Drop: 2 to 1 mix of protein to reservoir Complex formation by extensive soaking with AMPPNP solved in MgCl2 solution

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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: 0.92 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.81→90.731 Å / Num. obs: 70490 / % possible obs: 74.2 % / Redundancy: 41.6 % / Biso Wilson estimate: 33.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.152 / Net I/σ(I): 18.8
Reflection shellResolution: 1.81→1.99 Å / Rmerge(I) obs: 5.253 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3524 / CC1/2: 0.648

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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: 1.81→56.1 Å / SU ML: 0.1992 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4658
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2179 1987 2.82 %
Rwork0.1799 68473 -
obs0.1809 70460 74.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.02 Å2
Refinement stepCycle: LAST / Resolution: 1.81→56.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5577 0 125 308 6010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00945890
X-RAY DIFFRACTIONf_angle_d1.03737999
X-RAY DIFFRACTIONf_chiral_restr0.0651822
X-RAY DIFFRACTIONf_plane_restr0.00971014
X-RAY DIFFRACTIONf_dihedral_angle_d14.26372201
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.632389258714 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.850.921360.3354238X-RAY DIFFRACTION3.67
1.85-1.90.3219260.2842829X-RAY DIFFRACTION12.79
1.91-1.960.3707410.25731397X-RAY DIFFRACTION21.48
1.96-2.020.2868670.22542429X-RAY DIFFRACTION37.27
2.02-2.10.24531230.22564251X-RAY DIFFRACTION65.08
2.1-2.180.26271840.21126134X-RAY DIFFRACTION93.93
2.18-2.280.27271910.19336533X-RAY DIFFRACTION100
2.28-2.40.20651890.18656558X-RAY DIFFRACTION100
2.4-2.550.23711940.19096569X-RAY DIFFRACTION100
2.55-2.750.22011890.19726573X-RAY DIFFRACTION99.97
2.75-3.020.25221920.18856627X-RAY DIFFRACTION100
3.02-3.460.19551860.17516653X-RAY DIFFRACTION99.99
3.46-4.360.19972010.15386706X-RAY DIFFRACTION100
4.36-56.10.20241980.17776976X-RAY DIFFRACTION99.67
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)
12.8383777402-0.4501251069661.004958413980.929224039345-0.5707399393851.592886638180.202084022520.00765642298664-0.0703865414047-0.139489562707-0.192204004344-0.09217909971350.09721772630640.233892803151-5.45251758316E-50.2502871473530.03461079969780.02610033597410.279688388145-0.01476457901650.2336934191542.14204212962-48.915240341115.5461010201
20.520307978867-0.3175981361360.0267892305340.235472874977-0.06226270601570.0868791354569-0.390477510834-0.9052385257950.06496417735940.7383260764980.2278035593060.02789754761680.229417829460.0613307118049-0.04994983018190.4926149773870.0901055159997-0.02848747336030.710179901289-0.1293661324770.3345285648452.18974961728-39.335122060732.5021769031
31.87502633556-0.98568711195-0.5221328757061.68025075618-0.08328458852882.36502015023-0.102784872082-0.3346692855110.06903848431330.1408109735770.1575505152190.150656374615-0.000701469054976-0.152148184880.004856981873610.1802984056440.07361993581940.01263430053310.266995799698-0.02378539748680.208356121369-17.7769191222-39.089453673326.1704462705
41.052202364830.04776251347610.5305087298630.597685370148-0.1646214142641.96903970663-0.1231549769690.1249452703260.00166317966504-0.3852172569930.108295953546-0.00190780195422-0.2184265049250.02396103377794.79441082595E-60.219961820473-0.02430822157780.05244553919540.241080773153-0.01738512109280.206922139691-16.7830326358-66.554523102739.3979395716
51.564062386550.993058021341-0.08657230531650.8753375681620.5928834743981.63081851405-0.323442443628-0.1222227248430.04315258366760.5020983599270.03451902511920.1428877885210.122916219657-0.0502281452133-0.0008518409483740.2830154496820.01002430099330.01090513485390.237049363523-0.02163281935060.299075015054-12.3081765191-54.666106987253.7471490113
60.1894561461880.1362652909870.07924188558610.513768378607-0.1869568125710.378555061098-0.2121952011070.124152112744-0.0601001489116-0.22795175350.106059769367-0.110389483396-0.1299364054550.06019781675311.09767884644E-60.262524927167-0.06045825270320.03379116800980.262074718353-0.02163748459440.283280981809-14.344507395-59.730040454444.2230356248
70.9411992986020.511982185555-0.5737807992321.23773292907-0.6281848525770.4338423027060.107357153694-0.4238771638620.1280633434710.385846234842-0.1392874257980.264363056958-0.256579968978-0.035196620486-0.00128480360370.284940517242-0.04209931071750.05309869762130.395364792893-0.03459746394290.310129259082-28.1347979879-66.132893597257.8909777625
81.439302806740.252856393258-0.1631730621072.13748205425-0.4531091506851.462598204830.0311213070545-0.223325373003-0.05736766227880.226148608728-0.007286002379-0.08399721056090.001249054966840.08512315569972.86681230527E-50.192523897379-0.0466712252723-0.01729095586980.279922723791-0.01061563165480.230729488907-19.6326348137-77.261272077954.8167265975
90.8254842254930.469503502317-0.06311219655890.3801744091230.113157888631.78928076096-0.0210188384117-0.393210508151-0.9689742321210.0137817747593-0.208282351212-0.4397364362690.6198150344340.6807396077680.07476058388480.4825973643580.00893978839334-0.004758267870560.4056162492770.1001106958160.53776367901-16.9049361258-96.926305836655.9031695005
101.558591378930.56202726822-0.2273896500971.626011075170.1966710068370.7339545629610.0823723857534-0.332664382813-0.0184371372610.1911210450460.07155389249860.3061657375330.227810831198-0.2810277909020.002680759009910.264384125724-0.1082442586230.03324300184230.3947296190790.03426506718260.289161774658-34.0174233799-82.147286508159.0851151914
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 108 )AA2 - 1081 - 107
22chain 'A' and (resid 109 through 129 )AA109 - 129108 - 128
33chain 'A' and (resid 130 through 329 )AA130 - 329129 - 328
44chain 'B' and (resid 2 through 44 )BC2 - 441 - 43
55chain 'B' and (resid 45 through 74 )BC45 - 7444 - 73
66chain 'B' and (resid 75 through 108 )BC75 - 10874 - 107
77chain 'B' and (resid 109 through 149 )BC109 - 149108 - 148
88chain 'B' and (resid 150 through 249 )BC150 - 249149 - 248
99chain 'B' and (resid 250 through 280 )BC250 - 280249 - 279
1010chain 'B' and (resid 281 through 329 )BC281 - 329280 - 328

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