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- PDB-9fbm: Structure of human protein kinase CK2 catalytic subunit (CK2alpha... -

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Basic information

Entry
Database: PDB / ID: 9fbm
TitleStructure of human protein kinase CK2 catalytic subunit (CK2alpha, CSNK2A1 gene product) in complex with the cyclic peptidomimetic compound 12 discovered by high-throughput screening
Components
  • Casein kinase II subunit alpha
  • Cyclic peptidomimetic compound FMP37
KeywordsTRANSFERASE / human protein kinase ck2 catalytic subunit alpha / csnk2a1 gene product / inhibition of ck2alpha/ck2beta subunit interaction
Function / homology
Function and homology information


regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins ...regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of signal transduction by p53 class mediator / 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 / Regulation of PTEN stability and activity / Wnt signaling pathway / positive regulation of protein catabolic process / KEAP1-NFE2L2 pathway / kinase activity / 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
NICOTINIC ACID / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.054 Å
AuthorsWerner, C. / Niefind, K. / Pietsch, M. / Eimermacher, S. / Lindenblatt, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/11-1 Germany
Citation
Journal: To Be Published
Title: Discovery and characterization of a novel class of cyclic peptidic compounds inhibiting the assembly of the protein kinase CK2alpha2/beta2 holoenzyme
Authors: Werner, C. / Eimermacher, S. / Lindenblatt, D. / Niefind, K. / Pietsch, M.
#1: Journal: Biol.Chem. / Year: 2025
Title: A CK2 alpha ' mutant indicating why CK2 alpha and CK2 alpha ', the isoforms of the catalytic subunit of human protein kinase CK2, deviate in affinity to CK2 beta.
Authors: Werner, C. / Eimermacher, S. / Harasimowicz, H. / Fischer, D. / Pietsch, M. / Niefind, K.
#2: Journal: ACS Chem Biol / Year: 2013
Title: First structure of protein kinase CK2 catalytic subunit with an effective CK2beta-competitive ligand.
Authors: Raaf, J. / Guerra, B. / Neundorf, I. / Bopp, B. / Issinger, O.G. / Jose, J. / Pietsch, M. / Niefind, K.
History
DepositionMay 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: Structure summary / Category: struct / Item: _struct.title

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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
C: Casein kinase II subunit alpha
F: Cyclic peptidomimetic compound FMP37
G: Cyclic peptidomimetic compound FMP37
H: Cyclic peptidomimetic compound FMP37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,62621
Polymers127,2506
Non-polymers1,37615
Water13,781765
1
A: Casein kinase II subunit alpha
F: Cyclic peptidomimetic compound FMP37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9478
Polymers42,4172
Non-polymers5306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
G: Cyclic peptidomimetic compound FMP37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8517
Polymers42,4172
Non-polymers4345
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Casein kinase II subunit alpha
H: Cyclic peptidomimetic compound FMP37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8286
Polymers42,4172
Non-polymers4114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.016, 208.360, 76.718
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-405-

NA

21B-735-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 159 or resid 161...
d_2ens_1(chain "B" and (resid 2 through 159 or resid 161...
d_3ens_1(chain "C" and (resid 2 through 159 or resid 161...

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_11SERSERPROPROAA2 - 15916 - 173
d_12ASNASNGLYGLYAA161 - 235175 - 249
d_13ASPASPHISHISAA237 - 276251 - 290
d_14ARGARGHISHISAA278 - 286292 - 300
d_15GLUGLUGLNGLNAA288 - 310302 - 324
d_16ARGARGALAALAAA312 - 332326 - 346
d_17NIONIONIONIOAG401
d_21SERSERPROPROBB2 - 15916 - 173
d_22ASNASNGLYGLYBB161 - 235175 - 249
d_23ASPASPHISHISBB237 - 276251 - 290
d_24ARGARGHISHISBB278 - 286292 - 300
d_25GLUGLUGLNGLNBB288 - 310302 - 324
d_26ARGARGALAALABB312 - 332326 - 346
d_27NIONIONIONIOBM401
d_31SERSERPROPROCC2 - 15916 - 173
d_32ASNASNGLYGLYCC161 - 235175 - 249
d_33ASPASPHISHISCC237 - 276251 - 290
d_34ARGARGHISHISCC278 - 286292 - 300
d_35GLUGLUGLNGLNCC288 - 310302 - 324
d_36ARGARGALAALACC312 - 332326 - 346
d_37NIONIONIONIOCR401

NCS oper:
IDCodeMatrixVector
1given(-0.99898514473, 0.0447541554114, -0.00507406963997), (-0.0426281780958, -0.975830146354, -0.214332367827), (-0.0145436942188, -0.21389855315, 0.976747608095)0.683412947582, 136.558299047, 16.0161785921
2given(-0.999239864651, 0.0388331822228, -0.00341714069911), (0.0381878689396, 0.992701129823, 0.114394726777), (0.00783451070302, 0.11417727798, -0.993429499076)-38.3526302253, 35.1897828491, -0.479241582354

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Components

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Protein / Protein/peptide , 2 types, 6 molecules ABCFGH

#1: Protein Casein kinase II subunit alpha


Mass: 41685.426 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1 / Production host: Escherichia coli (E. coli)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Protein/peptide Cyclic peptidomimetic compound FMP37


Mass: 731.301 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) synthetic construct (others)

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Non-polymers , 4 types, 780 molecules

#3: Chemical ChemComp-NIO / NICOTINIC ACID


Mass: 123.109 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C6H5NO2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 765 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: protein solution: 97.5 mikroliter CK2alpha-1-335 solution (7 mg/ml in 500 mmol/l NaCl, 25 mmol/l Tris/HCl, pH 8.5) was mixed with 2.5 mikroliter 20 millimolar FMP37 in DMSO and incubated for ...Details: protein solution: 97.5 mikroliter CK2alpha-1-335 solution (7 mg/ml in 500 mmol/l NaCl, 25 mmol/l Tris/HCl, pH 8.5) was mixed with 2.5 mikroliter 20 millimolar FMP37 in DMSO and incubated for 30 min. reservoir: 1.5 mol/l lithium sulphate, 100 mM sodium HEPES buffer, pH 7.5. crystallization drop: 4 microliter protein solution plus 2 microliter reservoir.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.054→76.718 Å / Num. obs: 68956 / % possible obs: 87.5 % / Redundancy: 35.3 % / Biso Wilson estimate: 21.56 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.562 / Rpim(I) all: 0.095 / Rrim(I) all: 0.57 / Rsym value: 0.562 / Net I/σ(I): 9.6
Reflection shellResolution: 2.054→2.182 Å / Redundancy: 37.4 % / Rmerge(I) obs: 6.641 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3448 / CC1/2: 0.563 / Rpim(I) all: 1.116 / Rrim(I) all: 6.738 / Rsym value: 6.641 / % possible all: 26.8

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Processing

Software
NameVersionClassification
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
PHENIX1.21_5207refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.054→54.7 Å / SU ML: 0.2361 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.733
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2388 1023 1.48 %
Rwork0.1847 67912 -
obs0.1855 68935 87.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.82 Å2
Refinement stepCycle: LAST / Resolution: 2.054→54.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8387 0 226 765 9378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078892
X-RAY DIFFRACTIONf_angle_d0.899512046
X-RAY DIFFRACTIONf_chiral_restr0.05681234
X-RAY DIFFRACTIONf_plane_restr0.00771546
X-RAY DIFFRACTIONf_dihedral_angle_d12.91523340
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.790767879704
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.816510107953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.054-2.160.3998330.24192088X-RAY DIFFRACTION19.11
2.16-2.30.29581540.248710179X-RAY DIFFRACTION92.96
2.3-2.480.29061640.223710954X-RAY DIFFRACTION99.48
2.48-2.720.27041620.209110974X-RAY DIFFRACTION99.64
2.72-3.120.25931640.205111051X-RAY DIFFRACTION99.8
3.12-3.930.20721710.159111154X-RAY DIFFRACTION99.95
3.93-54.70.1991750.149511512X-RAY DIFFRACTION99.86
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)
10.7308307570120.07807039777540.03898616555460.604263448767-0.3496074170411.61244496304-0.0127336940006-0.122725117249-0.1328125790170.128640112806-0.0936835212836-0.1692830004890.09443842642590.1323615525210.07110074990120.2087717184920.0436218092166-0.007854519097710.163667164490.0504694484130.1379348524673.6545404529752.0123677229-18.0961639156
22.784505825260.1107904746820.6838542410481.93317391977-0.2634645943753.662275516120.03214741543170.09018929775210.04372967649620.178234913871-0.02898782224880.0563877380793-0.174036454589-0.7358217402590.04239068749160.1987011170550.01984080439360.04305853504820.1467698756980.05716049342950.102154830985-3.4829393429362.620606525-32.1892241117
31.10565233449-0.276841985559-0.2857198195192.34867013989-1.175908072351.230825264630.04773355346480.1681980743150.0284416980455-0.0192953251659-0.150176046224-0.2646312560360.1134898460710.1172261555970.08345390573470.1859807185840.005339812521710.003410387442810.1268945676790.006599116363660.07533701070982.9568089360856.5331445666-25.6088287938
45.51830753562.66853102418-0.1523253281622.617358742340.01709103547770.6504602399120.05588344559410.2596870279940.0450530465377-0.09388311174430.07900143860850.5673167380490.289251142959-0.632937246574-0.08232130770670.228185131285-0.0805405178426-0.05836531422130.4002498456560.05255836702610.240950217599-14.868301366653.8009519109-30.7987127232
50.498137317898-0.04708361988230.3095548904180.4826237444140.1089545857380.240032563165-0.06618146541780.403645212749-0.177310597602-0.297125948665-0.02360050839930.1539913648480.280195166476-0.263983232946-0.05637385423280.312267239847-0.107459518493-0.03666607104830.31190540816-0.05928925330080.146114364786-13.568253298345.8702928032-24.6060995204
61.81222783267-0.139345791756-1.069334614620.815114916412-0.3931042093081.546809640290.126100887303-0.05939253777980.1126736564550.25098692025-0.004904958550210.135490391015-0.0674237805206-0.253708727372-0.09739215054180.244401976051-0.04551160112750.02308517059640.2257472040490.0132990549810.101404357356-17.902423668853.992202875-5.99433739311
71.128145749650.478008591981.094722288861.153009712390.7850434646761.30449709396-0.01207863607920.126054304765-0.299589679202-0.148063209222-0.007655649215810.1477675454390.407894941963-0.635022421951-0.1053048778410.391991124873-0.2254154896160.0115828452460.396661606216-0.02170237092740.205980137827-24.276134799639.7252750182-15.2170418967
80.4090137384810.3744716447840.1041729657860.9201341663390.9943430692281.43491317352-0.183015378519-0.1175761198780.03884388765640.0173747965877-0.01467889021390.201167548225-0.238397416759-0.4136026342550.02438993302210.2397749042610.0781409893624-0.06921468018620.191076483939-0.02999739041980.177808014946-1.409041917791.1953583477-5.32614674949
91.086137124430.377417707985-0.239765749150.99587360941.021170562621.99678473946-0.2025844355050.0760494395656-0.0317126577879-0.2259715896750.0414545053294-0.0421800936049-0.2199676218110.1261852191210.1545499417870.297132315378-0.0441212769794-0.0355494187910.15452468903-0.0002455108143840.1439440906883.5942858674984.6281979622-26.4299817322
101.71145589110.8174981010110.3813675978751.154445168330.007755860393680.123096493321-0.1038679037390.230994187273-0.131403880225-0.10215154310.177558663925-0.572022011835-0.3425685623010.602828122548-0.113102239060.427666755135-0.2751970933220.03562185424070.485581368594-0.1028922632040.33354433076818.063317911191.0721752916-25.1805740812
110.529769272270.1955335124020.04393410281240.7678123156160.08513773047970.947734068845-0.3143419966220.07041430960390.0584171506709-0.07479779061240.0743171697168-0.366124979301-0.4890217680690.435790026257-0.2361701237240.265081580124-0.136900167649-0.1136144683660.0930812464970.03399109084690.33404907355121.384709757392.6558261881-6.20701700434
120.6146495993410.0763645134072-0.1948612281220.4933820346410.4925293427281.473663543465.27382620548E-5-0.3906133372010.07073772945030.08600483176460.1885015102730.251311242343-0.107342489373-0.269415549563-0.007879020901110.1669569307540.05014869376250.0241377143090.6557623890240.115194143360.391192153551-37.421769493888.333470223328.9128695332
131.233155363410.04449630789090.03693591673030.61514912555-0.2735817999540.8772862694670.0241692994153-0.201816302940.007273168513-0.02687531176110.1688224167160.2262105799560.0308555601123-0.228332196358-0.0308713397880.0836799926956-0.0183927561036-0.01969007310190.2150568335290.08238989394610.166150636972-19.753994647481.896781114920.1036336546
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 108 )AA75 - 10874 - 107
44chain 'A' and (resid 109 through 129 )AA109 - 129108 - 128
55chain 'A' and (resid 130 through 173 )AA130 - 173129 - 172
66chain 'A' and (resid 174 through 280 )AA174 - 280173 - 279
77chain 'A' and (resid 281 through 332 )AA281 - 332280 - 331
88chain 'B' and (resid 1 through 35 )BE1 - 351 - 35
99chain 'B' and (resid 36 through 108 )BE36 - 10836 - 108
1010chain 'B' and (resid 109 through 129 )BE109 - 129109 - 129
1111chain 'B' and (resid 130 through 332 )BE130 - 332130 - 332
1212chain 'C' and (resid 2 through 87 )CG2 - 871 - 86
1313chain 'C' and (resid 88 through 332 )CG88 - 33287 - 331

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