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- PDB-8qqb: Crystal structure of protein kinase CK2 catalytic subunit in comp... -

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Basic information

Entry
Database: PDB / ID: 8qqb
TitleCrystal structure of protein kinase CK2 catalytic subunit in complex with a Dibromo Dihydro Dibenzofuranone derivative
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / protein kinase CK2 casein kinase II catalytic subunit CK2alpha dibenzofuranone inhibitors
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 / Maturation of hRSV A proteins / Sin3-type complex ...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 / Maturation of hRSV A proteins / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / 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 / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / 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
: / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsWerner, C. / Niefind, K. / Jose, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/11-1 Germany
Citation
Journal: Acs Pharmacol Transl Sci / Year: 2024
Title: Discovery of 7,9-Dibromo-dihydrodibenzofuran as a Potent Casein Kinase 2 (CK2) Inhibitor: Synthesis, Biological Evaluation, and Structural Studies on E- / Z -Isomers.
Authors: Rumler, H. / Schmithals, C. / Werner, C. / Bollacke, A. / Aichele, D. / Gotz, C. / Niefind, K. / Wunsch, B. / Jose, J.
#1: Journal: Pharmaceuticals (Basel) / Year: 2018
Title: A pi-Halogen Bond of Dibenzofuranones with the Gatekeeper Phe113 in Human Protein Kinase CK2 Leads to Potent Tight Binding Inhibitors.
Authors: Schnitzler, A. / Gratz, A. / Bollacke, A. / Weyrich, M. / Kucklaender, U. / Wuensch, B. / Goetz, C. / Niefind, K. / Jose, J.
#2: Journal: Mol Cell Biochem / Year: 2011
Title: Identification of novel CK2 inhibitors with a benzofuran scaffold by novel non-radiometric in vitro assays.
Authors: Gratz, A. / Kucklaender, U. / Bollig, R. / Goetz, C. / Jose, J.
History
DepositionOct 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 1, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,25215
Polymers83,3712
Non-polymers1,88113
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-100 kcal/mol
Surface area30450 Å2
Unit cell
Length a, b, c (Å)128.242, 128.242, 124.547
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 258 or resid 260 through 402 or resid 403))
d_2ens_1(chain "B" and (resid 2 through 258 or resid 260 through 402 or resid 403))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-IDBeg label alt-IDEnd label alt-ID
d_11SERILEA1 - 257
d_12LYSGLNA259 - 330
d_13EDOEDOB
d_14W32W32DBB
d_21SERILEF1 - 257
d_22LYSGLNF259 - 330
d_23EDOEDOG
d_24W32W32IBB

NCS oper: (Code: givenMatrix: (0.00405317796316, -0.999989465139, 0.00215438150348), (0.997981826973, 0.00390849489528, -0.0633797814664), (0.0633706933801, 0.00240692312239, 0.997987155199)Vector: - ...NCS oper: (Code: given
Matrix: (0.00405317796316, -0.999989465139, 0.00215438150348), (0.997981826973, 0.00390849489528, -0.0633797814664), (0.0633706933801, 0.00240692312239, 0.997987155199)
Vector: -62.7759349298, 63.4531318669, 32.32792218)

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Components

#1: Protein Casein kinase II subunit alpha


Mass: 41685.426 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-WJE / (4~{Z})-7,9-bis(bromanyl)-8-oxidanyl-4-(phenylazanylmethylidene)-1,2-dihydrodibenzofuran-3-one


Mass: 463.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H13Br2NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 3.24 Å3/Da / Density % sol: 62.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Initial drops were prepared by mixing two parts of a solution of 5 mg per mL CK2alpha1-335 including 1 mM 12c together with one part of the reservoir solution containing 30 % (weight per ...Details: Initial drops were prepared by mixing two parts of a solution of 5 mg per mL CK2alpha1-335 including 1 mM 12c together with one part of the reservoir solution containing 30 % (weight per volume), PEG8000, 0.2 M (NH4)2SO4, and 0.1 M sodium cacodylate, pH 6.5. Crystallization was induced by microseeding.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.26→57.01 Å / Num. obs: 29856 / % possible obs: 60.72 % / Redundancy: 12 % / Biso Wilson estimate: 41.27 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.318 / Rpim(I) all: 0.095 / Rrim(I) all: 0.332 / Net I/σ(I): 8.4
Reflection shellResolution: 2.26→2.341 Å / Rmerge(I) obs: 3.726 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 209 / CC1/2: 0.647 / Rpim(I) all: 1.106 / Rrim(I) all: 3.889 / % possible all: 4.32

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→57.01 Å / SU ML: 0.2472 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.1743
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2389 1454 4.87 %
Rwork0.2011 28402 -
obs0.2029 29856 60.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.99 Å2
Refinement stepCycle: LAST / Resolution: 2.26→57.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5576 0 102 165 5843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00155897
X-RAY DIFFRACTIONf_angle_d0.43977990
X-RAY DIFFRACTIONf_chiral_restr0.0418806
X-RAY DIFFRACTIONf_plane_restr0.00441020
X-RAY DIFFRACTIONf_dihedral_angle_d11.07372197
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.681211775214 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.340.506790.3477195X-RAY DIFFRACTION4.19
2.34-2.430.3401180.2985350X-RAY DIFFRACTION7.61
2.43-2.540.3414250.2998610X-RAY DIFFRACTION13.17
2.54-2.670.3592630.30471384X-RAY DIFFRACTION29.6
2.67-2.840.29941380.29792714X-RAY DIFFRACTION58.24
2.84-3.060.28672000.26053998X-RAY DIFFRACTION85.59
3.06-3.370.29182450.2344695X-RAY DIFFRACTION100
3.37-3.860.252400.18224713X-RAY DIFFRACTION100
3.86-4.860.18222250.15874789X-RAY DIFFRACTION100
4.86-57.010.22152910.19144954X-RAY DIFFRACTION99.81
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)
11.54906440797-1.896183547720.8051999161966.11467832144-2.466075810542.97610117167-0.0876754978192-0.170584259325-0.0127259238270.2098020792510.1312076088530.364032483079-0.215526413999-0.15379824676-0.07002267289520.2311194007170.01416891863940.0396959038940.319694701527-0.004152069433230.238234568659-49.35202732112.08608262737-13.4266287427
22.56547086713-1.04181517456-0.3250359736934.038484671710.8749333329941.798443856630.1447296033530.3352211142110.299165919751-0.578600555731-0.0697160845852-0.0592459489054-0.333696105421-0.0465069251612-0.08563026581480.3118419006690.02805085972810.01512674237510.3005982227810.06582024857450.2367072637-41.6564663039-2.23378475007-21.8058834564
33.37518018065-0.36272150852-1.027705043543.86249283835-0.1103491827673.46277680807-0.07580735202170.447307371514-0.227952298989-0.4501130771490.01001394999030.04585872612640.170235582286-0.2237719498580.05792339635620.3084893975490.0718799243665-0.02275798600420.276464031915-0.006933030352520.24288827924-39.2573146591-21.2165432018-26.957407756
44.946252139271.263658635052.157868387031.486473444750.6419722940552.369042415340.181797703772-0.334846886871-0.2837534398820.233874862236-0.1546247372460.09376286732280.242027444954-0.358478490153-0.02587066052830.3153832208980.005887073435110.06776682243250.3264097445620.01202750571930.222740749111-66.309439593215.123163100715.4791492352
53.0231241183.64398820666-3.430207250534.49582858111-4.337606134964.278642413-0.7314474312241.00195130632-0.199942307085-1.317539019560.163669074348-0.5155591127820.642713964094-0.4899942297350.5447729659910.736460856282-0.1117579728680.04096529486960.6961865427270.03211093736840.485886775388-65.891470594324.7968912889-0.878923779816
62.501556631530.449671115031-0.755296259572.52663147544-0.5595791023963.51528876028-0.008087786781970.3104788145970.0879177824769-0.2172225262140.08439923003-0.05024101501090.01499615473610.0386733889329-0.07400923638330.224853638754-0.0666522325034-0.001178827025480.288781393336-0.0004940622753360.244978487085-46.73381872625.54562978034.93538624793
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 197 )AA88 - 19787 - 196
33chain 'A' and (resid 198 through 331 )AA198 - 331197 - 330
44chain 'B' and (resid 2 through 108 )BF2 - 1081 - 107
55chain 'B' and (resid 109 through 129 )BF109 - 129108 - 128
66chain 'B' and (resid 130 through 331 )BF130 - 331129 - 330

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