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- PDB-7a4c: Crystal structure of human protein kinase CK2alpha (CSNK2A1 gene ... -

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Basic information

Entry
Database: PDB / ID: 7a4c
TitleCrystal structure of human protein kinase CK2alpha (CSNK2A1 gene product) in complex with the ATP-competitive inhibitor 5,6,7-tribromo-1H-triazolo[4,5-b]pyridine
ComponentsCasein kinase II subunit alphaCasein kinase 2
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2 / ATP-competitive inhibitor
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 / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...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 / Sin3-type complex / Synthesis of PC / 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 / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / peptidyl-threonine phosphorylation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of protein catabolic process / rhythmic process / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / protein stabilization / regulation of cell cycle / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / positive regulation of cell population proliferation / 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
Chem-QWW / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsNiefind, K. / Lindenblatt, D. / Toelzer, C. / Bretner, M. / Chojnacki, K. / Wielechowska, M. / Winska, P.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/4-2 Germany
Citation
Journal: Bioorg.Chem. / Year: 2021
Title: Synthesis, biological properties and structural study of new halogenated azolo[4,5-b]pyridines as inhibitors of CK2 kinase.
Authors: Chojnacki, K. / Lindenblatt, D. / Winska, P. / Wielechowska, M. / Toelzer, C. / Niefind, K. / Bretner, M.
#1: Journal: Bioorg. Chem. / Year: 2018
Title: Biological properties and structural study of new aminoalkyl derivatives of benzimidazole and benzotriazole, dual inhibitors of CK2 and PIM1 kinases.
Authors: Chojnacki, K. / Winska, P. / Wielechowska, M. / Lukowska-Chojnacka, E. / Toelzer, C. / Niefind, K. / Bretner, M.
#2: Journal: ACS Omega / Year: 2019
Title: Diacritic Binding of an Indenoindole Inhibitor by CK2alpha Paralogs Explored by a Reliable Path to Atomic Resolution CK2alpha' Structures.
Authors: Lindenblatt, D. / Nickelsen, A. / Applegate, V.M. / Hochscherf, J. / Witulski, B. / Bouaziz, Z. / Marminon, C. / Bretner, M. / Le Borgne, M. / Jose, J. / Niefind, K.
#3: Journal: J. Med. Chem. / Year: 2020
Title: Structural and Mechanistic Basis of the Inhibitory Potency of Selected 2-Aminothiazole Compounds on Protein Kinase CK2.
Authors: Lindenblatt, D. / Nickelsen, A. / Applegate, V.M. / Jose, J. / Niefind, K.
History
DepositionAug 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 13, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)81,70013
Polymers80,1332
Non-polymers1,56611
Water3,153175
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8967
Polymers40,0671
Non-polymers8296
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8046
Polymers40,0671
Non-polymers7375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.681, 127.681, 126.296
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 335))
d_2ens_1(chain "B" and (resid 2 through 7 or resid 9 through 335))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERSERA1 - 6
d_12ens_1ALAGLYA8 - 334
d_21ens_1SERSERB1 - 6
d_22ens_1ALAGLYB9 - 335

NCS oper: (Code: givenMatrix: (0.00633612699082, -0.997707503261, 0.0673764901973), (0.999939519348, 0.00692717828105, 0.0085423560654), (-0.00898950170152, 0.0673182897704, 0.997691052742)Vector: - ...NCS oper: (Code: given
Matrix: (0.00633612699082, -0.997707503261, 0.0673764901973), (0.999939519348, 0.00692717828105, 0.0085423560654), (-0.00898950170152, 0.0673182897704, 0.997691052742)
Vector: -65.1630605708, -62.7792420554, 32.0118742767)

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Components

#1: Protein Casein kinase II subunit alpha / Casein kinase 2 / CK II alpha


Mass: 40066.742 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-QWW / 5,6,7-tris(bromanyl)-1~{H}-[1,2,3]triazolo[4,5-b]pyridine


Mass: 356.800 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5HBr3N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3.22 Å3/Da / Density % sol: 61.83 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1 MIKROLITER OF THE CK2ALPHA/INHIBITOR MIXTURE (COMPOSITION: 7 MG/ML CK2ALPHA ENZYME, 1 MILLIMOLAR INHIBITOR, 10 % DIMETHYL SULFOXIDE, 450 MM NACL, 22.5 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 1 ...Details: 1 MIKROLITER OF THE CK2ALPHA/INHIBITOR MIXTURE (COMPOSITION: 7 MG/ML CK2ALPHA ENZYME, 1 MILLIMOLAR INHIBITOR, 10 % DIMETHYL SULFOXIDE, 450 MM NACL, 22.5 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 1 MIKROLITER RESERVOIR SOLUTION (COMPOSITION: 25 % PEG3350, 0.2 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS BUFFER, PH 5.5) FOLLOWED BY VAPOUR DIFFUSION EQUILIBRATION AGAINST THE RESERVOIR SOLUTION.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 2.502→90.284 Å / Num. obs: 28550 / % possible obs: 78 % / Redundancy: 7.5 % / Biso Wilson estimate: 43.98 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.067 / Rrim(I) all: 0.186 / Rsym value: 0.173 / Net I/σ(I): 9.2
Reflection shellResolution: 2.502→2.725 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.007 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1428 / CC1/2: 0.617 / Rpim(I) all: 0.507 / Rrim(I) all: 1.132 / Rsym value: 1.007 / % possible all: 17.5

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PVR

2pvr


Resolution: 2.502→89.79 Å / SU ML: 0.2799 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1442
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2323 1139 3.99 %
Rwork0.2062 27387 -
obs0.2072 28526 77.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.89 Å2
Refinement stepCycle: LAST / Resolution: 2.502→89.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5634 0 72 175 5881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00165861
X-RAY DIFFRACTIONf_angle_d0.46967926
X-RAY DIFFRACTIONf_chiral_restr0.042811
X-RAY DIFFRACTIONf_plane_restr0.00311015
X-RAY DIFFRACTIONf_dihedral_angle_d12.8642205
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.506235478858 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.620.3664120.3643284X-RAY DIFFRACTION6.6
2.62-2.750.3464590.30231434X-RAY DIFFRACTION33.36
2.75-2.930.28571400.2853489X-RAY DIFFRACTION80.73
2.93-3.150.29331820.26184355X-RAY DIFFRACTION99.91
3.15-3.470.27541800.23044362X-RAY DIFFRACTION99.98
3.47-3.970.19771900.18544390X-RAY DIFFRACTION100
3.97-50.19911790.16164443X-RAY DIFFRACTION99.96
5-89.790.21511970.19984630X-RAY DIFFRACTION99.53
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)
10.683536702588-0.0726446079840.1221560699690.469296157092-0.1457721547370.4947957910550.113782521038-0.780310429634-0.2783184936460.126682172669-0.07938371057930.03472433570020.1569951324270.474727067283-0.01264766753440.329025786312-0.0337997890799-0.08214248551250.336489669140.03868551659520.34843578996213.6557151004-42.284238492727.7159235744
20.8637709921840.2811146545541.123141710151.099246284340.1165577308471.513291076660.2214024297370.165617309061-0.548650797007-0.01325992856130.0225095830480.229840686360.223361410926-0.294436362859-0.0001704487991340.31461309333-0.00921016087805-0.05180198358840.4972746889460.006928108705810.374907890365-9.48192016617-53.031468320412.3337219079
31.615958040640.7022677166280.134531466451.347218409280.3598935204381.69117695418-0.1002703709670.122957627956-0.1957325180280.208380650246-0.05922093434430.314308847325-0.0262987526999-0.286243369308-0.001609111167630.230665551189-0.0583803751956-0.03736184176930.221722625542-0.0184742263820.349168799688-7.33437931833-50.152204636315.8681075009
41.822318445371.05517065222-0.6460984628760.608655552424-0.3745600290640.227518058991-0.524304780291.134559134180.358267373499-0.566594770490.533397335947-0.0493416525040.009512337077130.0751332775648-0.009045062506130.630931293564-0.27309949041-0.1499841587110.7136609491620.1442665573530.360414183287-2.76661418081-40.96466396360.738495599733
53.298443846680.491121680252-0.4095125216531.39740530596-0.1173937254821.89872122323-0.07793853663890.369495333017-0.298746923873-0.2629139535780.0901747156611-0.1483147637590.1794672850960.08001278768214.92791808524E-50.347546899442-0.0948080008849-0.05513014262050.249342431516-0.0140889574650.32248494071215.7919317085-42.80930027637.52272580367
61.335279628370.8716108162770.01502557164222.62118965928-0.0299811817072.5785282883-0.01728450299250.4641675818220.322331511293-0.267313348463-0.0270174507383-0.0429039208713-0.249484496439-0.03241683501110.0007892750670190.321423119671-0.098957291776-0.04677807677860.3702555012130.05366786326840.3011351519215.4300045105-28.25078927663.93666647835
70.827881024649-0.573366722292-0.8563819214543.171927612231.703475480482.44142706722-0.118032228178-0.170196325611-0.1160038782710.21358415610.03399197903040.04806535367440.3044534180480.0635286053233-1.68575639529E-50.2940563702770.0236878358273-0.01611312637340.3286408701320.04173230348580.238096534432-14.8069626464-66.046379545146.0636315869
80.420857462132-0.5875260251390.4533139269320.814676887845-0.6274227690840.4840455870450.6042758894050.564426353027-0.374342386687-0.883806646937-0.4232895252180.260348900160.3876438124860.177592504143-0.06084446005470.5575344023230.123594014289-0.1468109272920.722609458624-0.09321479976320.349551625943-24.4031374806-66.087326362430.1648952596
91.49352730533-0.2445416162950.2425739957512.18519952783-0.391885924042.3270409540.1327762942120.1336649384490.059339824226-0.239865490043-0.0822353799870.0158064634866-0.1486906790930.06263666584010.0007877981240720.2634516661830.04975418020660.007648314042560.249183067931-0.04001362096730.231100296835-23.732105746-46.793649617235.0665198377
101.32358059331-1.11931443867-0.3441416753631.02075744655-0.02068623026122.442108049090.0806392492864-0.376631508431-0.1295517495220.0471344759493-0.08914614945410.3601561013830.000149867557944-0.385960731148-0.0007174066353870.2782467127910.0914337332006-0.01508795627630.331239632618-0.01014073704490.361522074374-37.3599177796-49.929791311740.0379604939
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 24 )AA2 - 241 - 23
22chain 'A' and (resid 25 through 58 )AA25 - 5824 - 57
33chain 'A' and (resid 59 through 108 )AA59 - 10858 - 107
44chain 'A' and (resid 109 through 129 )AA109 - 129108 - 128
55chain 'A' and (resid 130 through 280 )AA130 - 280129 - 279
66chain 'A' and (resid 281 through 335 )AA281 - 335280 - 334
77chain 'B' and (resid 2 through 108 )BB2 - 1081 - 108
88chain 'B' and (resid 109 through 129 )BB109 - 129109 - 129
99chain 'B' and (resid 130 through 304 )BB130 - 304130 - 304
1010chain 'B' and (resid 305 through 335 )BB305 - 335305 - 335

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