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- PDB-9hxu: Protein kinase CK2 catalytic subunit alpha (CSNK2A1 gene product)... -

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Basic information

Entry
Database: PDB / ID: 9hxu
TitleProtein kinase CK2 catalytic subunit alpha (CSNK2A1 gene product) in complex with F2X-Entry screen fragment C02
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / Protein kinase CK2 / kinase / fragment-based screening / ligand / casein kinase II
Function / homology
Function and homology information


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 / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / negative regulation of signal transduction by p53 class mediator ...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 / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / negative regulation of signal transduction by p53 class mediator / 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 / : / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / kinase activity / KEAP1-NFE2L2 pathway / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / DNA damage response / 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
2,4,5-tris(fluoranyl)-3-methoxy-benzoic acid / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWerner, C. / Harasimowicz, H. / Barthel, T. / Weiss, M.S. / Niefind, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/11-1 Germany
CitationJournal: Kinases Phosphatases / Year: 2026
Title: Crystallographic Fragment Screening with CK2 alpha', an Isoform of Human Protein Kinase CK2 Catalytic Subunit, and Its Use to Obtain a CK2 alpha'/Heparin Complex Structure
Authors: Werner, C. / Barthel, T. / Harasimowicz, H. / Marminon, C. / Weiss, M.S. / Borgne, M.L. / Niefind, K.
History
DepositionJan 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 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)85,80213
Polymers84,4762
Non-polymers1,32611
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-102 kcal/mol
Surface area30180 Å2
Unit cell
Length a, b, c (Å)128.877, 128.877, 123.798
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 7 or resid 9 through 258 or resid 260 through 401))
d_2ens_1(chain "B" and (resid 2 through 7 or resid 9 through 258 or resid 260 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_11SERSERSERSERAA2 - 722 - 27
d_12ALAALAILEILEAA9 - 25829 - 278
d_13LYSLYSALAALAAA260 - 332280 - 352
d_21SERSERSERSERBB2 - 722 - 27
d_22ALAALAILEILEBB9 - 25829 - 278
d_23LYSLYSALAALABB260 - 332280 - 352

NCS oper: (Code: givenMatrix: (5.05221312186E-6, -0.997552573542, -0.0699204047075), (0.999965614277, -0.000574795017762, 0.00827283953869), (-0.00829278227259, -0.06991804224, 0.997518269072)Vector: ...NCS oper: (Code: given
Matrix: (5.05221312186E-6, -0.997552573542, -0.0699204047075), (0.999965614277, -0.000574795017762, 0.00827283953869), (-0.00829278227259, -0.06991804224, 0.997518269072)
Vector: 65.3036593955, 63.0549695306, 32.7941748228)

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Components

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


Mass: 42238.102 Da / Num. of mol.: 2
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-SYA / 2,4,5-tris(fluoranyl)-3-methoxy-benzoic acid


Mass: 206.119 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H5F3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 3.04 Å3/Da / Density % sol: 59.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir:200 mM Li2SO4, 100 mM Bis-Tris/HCl, pH 6.5, 35 % (w/v) PEG 3350 Protein/Ligand mix: 5 mg per mL CK2alpha1-335, 100 mM ligand/0.5 mM CX-4945, 10 % DMSO prequilibrated Drop: 4 ...Details: Reservoir:200 mM Li2SO4, 100 mM Bis-Tris/HCl, pH 6.5, 35 % (w/v) PEG 3350 Protein/Ligand mix: 5 mg per mL CK2alpha1-335, 100 mM ligand/0.5 mM CX-4945, 10 % DMSO prequilibrated Drop: 4 microliter protein/ligand mix, 2 microliter reservoir solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / 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: 2.2→91.13 Å / Num. obs: 48185 / % possible obs: 90.8 % / Redundancy: 26.7 % / Biso Wilson estimate: 64.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.016 / Net I/σ(I): 23.3
Reflection shellResolution: 2.205→2.303 Å / Rmerge(I) obs: 2.997 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2409 / CC1/2: 0.492 / Rpim(I) all: 0.571

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
PHASER1.20.1_4487phasing
XDSdata reduction
Aimlessdata scaling
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→39.3 Å / SU ML: 0.2921 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8925
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2163 1205 2.5 %
Rwork0.1918 46934 -
obs0.1924 48139 90.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.07 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5586 0 78 80 5744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00195827
X-RAY DIFFRACTIONf_angle_d0.53137891
X-RAY DIFFRACTIONf_chiral_restr0.0442808
X-RAY DIFFRACTIONf_plane_restr0.00411012
X-RAY DIFFRACTIONf_dihedral_angle_d11.94582185
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.01171008801 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.290.3461490.31181940X-RAY DIFFRACTION34.23
2.29-2.40.31371190.26694639X-RAY DIFFRACTION82.2
2.4-2.520.29151510.25935663X-RAY DIFFRACTION99.93
2.52-2.680.32511420.27045686X-RAY DIFFRACTION100
2.68-2.890.29671500.26735694X-RAY DIFFRACTION99.98
2.89-3.180.27191490.23425693X-RAY DIFFRACTION99.83
3.18-3.640.26191420.21275769X-RAY DIFFRACTION100
3.64-4.580.19351510.16655828X-RAY DIFFRACTION100
4.58-39.30.16341520.15756022X-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)
12.10002270321-0.71073164602-0.6977071861640.7769604408790.1501683373061.51780457366-0.130408880630.1808206279160.104389826018-0.1367121630250.05887493374870.06483182133660.00633373524958-0.2984031264054.64078772337E-60.587268084010.02488164791820.01493509577960.563831311179-0.036639322560.566589816166-2.1195900158247.969374280518.1713884121
22.1524421247-0.3157174896480.3214581217592.191078048720.03747308117931.90665688294-0.0828157674881-0.162450418229-0.006210569794990.141089576610.111695079935-0.114722214060.06387545838850.20227682343-4.29664292558E-60.5126709405460.03986101211610.04499156280770.51796272027-0.02950152896640.50640955976617.171600597938.697842518526.1868082973
30.136951320366-0.1508233711390.1523283197550.167489344845-0.1609810607410.194357289161-0.1233752070150.1137625588640.0131345193887-0.2102446308230.06148876293210.225160534723-0.08973423144720.28545384294-9.80827983809E-50.645953344722-0.113850217703-0.0179112653460.6205712770860.1232169548830.63622676668521.798970882278.612292365934.8964118686
40.949305116250.277781625245-0.2244777497371.66555778898-0.2568451609320.83693197151-0.1705175664480.275706139358-0.029495946406-0.1489748019370.03045596506390.253000315170.5982986595990.01574852516470.0001026265993210.591807024496-0.0679790133875-0.005768888228450.5273311439170.04305370215810.623009698312.795864812756.076317706947.8099599281
51.25608542328-1.203583529270.07952724413981.656153896280.6290168709410.9981943016240.0195737489258-0.316115501199-0.191094117730.794696960485-0.1137373932850.3034670320120.04998834251310.542270812351-0.5116499199390.823003105889-0.184746299091-0.01379138181230.7344214099110.2757199819830.42957010413223.016373551561.6979835660.5864283383
61.941041883720.3413195915590.3252630662752.078916302530.6189376207291.478804429420.120832224902-0.2725962360510.1224893473670.294549514526-0.06354608179760.171036947574-0.006333836864170.03668865937644.99376160178E-50.523338986229-0.07928203932020.02580562541190.5867969565950.0794606459920.54004365859424.870043024580.491568249956.0538824933
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 129 )AA2 - 1291 - 128
22chain 'A' and (resid 130 through 332 )AA130 - 332129 - 331
33chain 'B' and (resid 2 through 24 )BD2 - 241 - 23
44chain 'B' and (resid 25 through 108 )BD25 - 10824 - 107
55chain 'B' and (resid 109 through 129 )BD109 - 129108 - 128
66chain 'B' and (resid 130 through 332 )BD130 - 332129 - 331

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