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- PDB-7psu: Structure of protein kinase CK2alpha mutant K198R associated with... -

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Basic information

Entry
Database: PDB / ID: 7psu
TitleStructure of protein kinase CK2alpha mutant K198R associated with the Okur-Chung Neurodevelopmental Syndrome
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2 / CSNK2A1 mutant K198R / Okur-Chung Neurodevelopmental Syndrome
Function / homology
Function and homology information


regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / : / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / rhythmic process / double-strand break repair / kinase activity / peptidyl-serine phosphorylation / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / positive regulation of cell population proliferation / apoptotic process / signal transduction / 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
Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsWerner, C. / Gast, A. / Lindenblatt, D. / Nickelsen, K. / Niefind, K. / Jose, J. / Hochscherf, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/4-2 Germany
CitationJournal: Front Mol Biosci / Year: 2022
Title: Structural and Enzymological Evidence for an Altered Substrate Specificity in Okur-Chung Neurodevelopmental Syndrome Mutant CK2 alpha Lys198Arg.
Authors: Werner, C. / Gast, A. / Lindenblatt, D. / Nickelsen, A. / Niefind, K. / Jose, J. / Hochscherf, J.
History
DepositionSep 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)96,31022
Polymers94,8162
Non-polymers1,49420
Water11,998666
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,23412
Polymers47,4081
Non-polymers82611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,07610
Polymers47,4081
Non-polymers6689
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.824, 127.824, 123.180
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
d_1ens_1(chain "A" and (resid 2 through 220 or resid 222 through 333 or resid 401 through 404))
d_2ens_1(chain "B" and (resid 2 through 220 or resid 222 through 333 or resid 402 through 405))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERCYSA1 - 219
d_12ens_1LEUARGA221 - 332
d_13ens_1EDOEDOB
d_14ens_1EDOEDOC
d_15ens_1EDOEDOD
d_16ens_1EDOEDOE
d_21ens_1SERCYSG1 - 219
d_22ens_1LEUARGG221 - 332
d_23ens_1EDOEDOH
d_24ens_1EDOEDOI
d_25ens_1EDOEDOJ
d_26ens_1EDOEDOK

NCS oper: (Code: givenMatrix: (0.008050919572, -0.997033362091, 0.0765484001891), (0.999967353957, 0.0080799830039, 6.99672190945E-5), (-0.000688269424194, 0.0765453378863, 0.99706586419)Vector: -64. ...NCS oper: (Code: given
Matrix: (0.008050919572, -0.997033362091, 0.0765484001891), (0.999967353957, 0.0080799830039, 6.99672190945E-5), (-0.000688269424194, 0.0765453378863, 0.99706586419)
Vector: -64.513990966, -62.1681353152, 32.71122664)

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Components

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


Mass: 47407.930 Da / Num. of mol.: 2 / Mutation: K198R
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 666 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.16 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The crystallization drops were composed of a 1:1 mix of the protein solution (5 mg/mL in 500 mM NaCl, 25 mM TRIS/HCl buffer, pH 8,5) and the reservoir solution containing [0.2 M lithium ...Details: The crystallization drops were composed of a 1:1 mix of the protein solution (5 mg/mL in 500 mM NaCl, 25 mM TRIS/HCl buffer, pH 8,5) and the reservoir solution containing [0.2 M lithium sulfate, 25 % (w/v) PEG 3350 and 0.1 M Bis/TRIS/HCl, pH 6.5]. The crystals were optimized by macroseeding and transferred into a cryo-protectant solution composed of 70 microliter of the reservoir solution and 30 microliter ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Apr 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.774→88.698 Å / Num. obs: 65649 / % possible obs: 66.5 % / Redundancy: 44.4 % / Biso Wilson estimate: 3.97 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.587 / Rpim(I) all: 0.087 / Rrim(I) all: 0.594 / Rsym value: 0.587 / Net I/σ(I): 18.1
Reflection shellResolution: 1.774→1.98 Å / Rmerge(I) obs: 2.814 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3280 / CC1/2: 0.709 / Rpim(I) all: 0.448 / Rrim(I) all: 2.85 / Rsym value: 2.814 / % possible all: 12

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata processing
autoPROCdata reduction
STARANISO2.3.73data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PVR

2pvr


Resolution: 1.77→50.9 Å / SU ML: 0.1676 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.2961
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2183 1332 2.03 %
Rwork0.1802 64295 -
obs0.1809 65627 66.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.22 Å2
Refinement stepCycle: LAST / Resolution: 1.77→50.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5612 0 83 666 6361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00385834
X-RAY DIFFRACTIONf_angle_d0.64747877
X-RAY DIFFRACTIONf_chiral_restr0.0465809
X-RAY DIFFRACTIONf_plane_restr0.00671008
X-RAY DIFFRACTIONf_dihedral_angle_d11.59782196
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.60761872272 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.8400.2662392X-RAY DIFFRACTION4.04
1.84-1.910.3267270.23451123X-RAY DIFFRACTION11.81
1.91-20.2389510.21852268X-RAY DIFFRACTION23.72
2-2.10.2662860.2054114X-RAY DIFFRACTION43.09
2.1-2.240.23541660.20267635X-RAY DIFFRACTION79.72
2.24-2.410.23711780.19279613X-RAY DIFFRACTION99.76
2.41-2.650.23632080.18519622X-RAY DIFFRACTION99.85
2.65-3.030.18932130.17499674X-RAY DIFFRACTION99.97
3.03-3.820.19861690.15619806X-RAY DIFFRACTION99.98
3.82-50.90.20342340.168910048X-RAY DIFFRACTION99.14
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)
10.978606869786-0.3242977424420.1013180447470.658016039012-0.007354061615680.8952512251420.0449473286609-0.0569042709894-0.01045138101090.0100665744301-0.0324930803765-0.02910379609120.03841021526270.128342216626-0.01864435973650.06060607383930.02159431886020.007727260480530.0801683736042-0.03095268593360.05315229856951.83136200068-48.693962946815.1865270831
20.260133442392-0.595334177554-0.1446381347481.609848053580.3224553360770.080162990433-0.214695596733-0.5678770857040.1725280849740.905457656808-0.04111889036150.5214118298830.0429108133859-0.3008804696350.235158194410.4521905580060.07776111164880.04606971308440.537212360183-0.1630834844970.3010809137731.50389236304-39.050195897831.4402625826
30.152311851652-0.0504576598796-0.08575964097460.3439458046370.1103167232150.255660935253-0.00400568472036-0.1860273750050.1409416081050.135319747590.08092540965230.0591901183911-0.0563355699804-0.03833551394980.1842354607950.05341723007950.1411737730140.07456450073460.124237251755-0.09795401219640.0738794220237-17.5429612213-38.271704496125.5639532421
40.3231902063540.326222652030.03357255105950.7405918099970.5422222477640.965101891055-0.07342350009330.0556698008169-0.0239375252726-0.1112243043020.129762123309-0.133395861924-0.1259407395840.110938998762-0.03743329003330.126542928259-0.02283830125130.01003260613830.0763387577458-0.01143690853690.0500846869929-16.7696835475-66.166806328238.7995924552
53.93934623759-0.355377163375-0.6354100718453.838556316640.9497618641554.01829717402-0.0363061346909-0.1655869557050.06785118048240.181222573656-0.0381389562620.118545493631-0.0955756402302-0.1481700902720.0439986641460.0871020047686-0.0433833952337-0.0363611406140.0869541041365-0.02621387514220.0804625018118-12.4096489294-54.365102354453.2012230487
60.746768381627-0.297446357351-0.03034382756210.897029788995-0.03214606354840.665967349729-0.00409299336049-0.008978566278760.09862394136610.0142082537993-0.0122395778413-0.131829697181-0.09191144277610.1280914878370.01336697202040.048266451397-0.03474683436220.01777883488650.0329372917383-0.003706803281690.030777573818-14.3726512159-59.313940783643.588973868
70.5957339631260.426192711904-0.4580860090750.610932463662-0.4383783533970.3919078904960.141008472019-0.3431511299490.09021840578070.262531269597-0.099866580970.0451383831653-0.1362722733830.162593903226-0.03523366871130.100116315785-0.03726852059610.03942456633040.15884482416-0.01214830485560.0774435051774-28.1178226971-65.711826622457.0805856851
80.6482336796640.399874457803-0.04138189840490.690206250833-0.1700899799960.8340290477240.057888221682-0.103166867062-0.0507008979420.0961969118895-0.0351584479336-0.0485323286706-0.03373728121370.007841619462830.01450366167130.038187462722-0.0345949118877-9.74271816557E-50.04277830861790.008419908166310.0439672968666-20.4080146525-74.597250824151.3735025391
92.88645303261-0.9304970605382.325481704862.05534534666-0.5946411737223.59218906679-0.01844600932740.03177684726530.03088195597870.1420595200620.00478328554146-0.0944946513762-0.0512984983260.1645243892410.04029393718150.133331438554-0.0530302093602-0.0523145618140.1435057804360.05828057736940.075215090785-16.9018095347-84.362633540763.8093109208
101.18814827455-0.116778544874-1.498988601472.346602186990.3841075405374.43025112477-0.0992911637857-0.27732406632-0.215398491330.0821567229023-0.0261633288435-0.6620791754730.3813250403750.5709069886790.1637556793430.2311767773970.00295530324648-0.04683925941420.1595115873070.08730369213630.346939728311-16.7459036538-96.10308704655.4666490038
110.9083205672060.262283924023-0.639872472790.505387640249-0.3539781266881.119491339580.0625974454779-0.03538732034750.08774866560450.0968160882340.02887238832490.142653811455-0.0732687710786-0.0877614637755-0.1123065302730.106638520119-0.09174206209260.01636438219930.1258183535770.04832948249480.091540660355-34.7705942303-80.37969626558.3053528524
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 333 )AA130 - 333129 - 332
44chain 'B' and (resid 2 through 44 )BG2 - 441 - 43
55chain 'B' and (resid 45 through 74 )BG45 - 7444 - 73
66chain 'B' and (resid 75 through 108 )BG75 - 10874 - 107
77chain 'B' and (resid 109 through 149 )BG109 - 149108 - 148
88chain 'B' and (resid 150 through 227 )BG150 - 227149 - 226
99chain 'B' and (resid 228 through 249 )BG228 - 249227 - 248
1010chain 'B' and (resid 250 through 280 )BG250 - 280249 - 279
1111chain 'B' and (resid 281 through 333 )BG281 - 333280 - 332

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