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- PDB-6tei: Crystal structure of human protein kinase CK2alpha (CSNK2A1 gene ... -

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Basic information

Entry
Database: PDB / ID: 6tei
TitleCrystal structure of human protein kinase CK2alpha (CSNK2A1 gene product) in complex with the 2-aminothiazole-type inhibitor 17
ComponentsCasein kinase II subunit alphaCasein kinase 2
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2 / ATP-competitive inhibitor / 2-aminothiazole derivative
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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 ...Casein Kinase 2, subunit alpha / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-N4N / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.756 Å
AuthorsNiefind, K. / Lindenblatt, D. / Jose, J. / Applegate, V.M. / Nickelsen, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationNI 643/4-2 Germany
Citation
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.
#1: Journal: ACS Omega / Year: 2019
Title: Diacritic Binding of an Indenoindole Inhibitor by CK2a Paralogs Explored by a Reliable Path to Atomic Resolution CK2a' 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.
History
DepositionNov 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _software.name
Revision 1.2Jan 24, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)84,2547
Polymers83,3712
Non-polymers8835
Water6,936385
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0793
Polymers41,6851
Non-polymers3932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1754
Polymers41,6851
Non-polymers4893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.891, 127.891, 124.334
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-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERHISHIS(chain 'A' and (resid 2 through 18 or resid 20...AA2 - 1816 - 32
12PROPROGLUGLU(chain 'A' and (resid 2 through 18 or resid 20...AA20 - 2734 - 41
13HISHISPHEPHE(chain 'A' and (resid 2 through 18 or resid 20...AA29 - 11343 - 127
14HISHISPROPRO(chain 'A' and (resid 2 through 18 or resid 20...AA115 - 295129 - 309
15ALAALAGLNGLN(chain 'A' and (resid 2 through 18 or resid 20...AA297 - 331311 - 345
26SERSERHISHIS(chain 'B' and (resid 2 through 18 or resid 20...BB2 - 1816 - 32
27PROPROGLUGLU(chain 'B' and (resid 2 through 18 or resid 20...BB20 - 2734 - 41
28HISHISPHEPHE(chain 'B' and (resid 2 through 18 or resid 20...BB29 - 11343 - 127
29HISHISPROPRO(chain 'B' and (resid 2 through 18 or resid 20...BB115 - 295129 - 309
210ALAALAGLNGLN(chain 'B' and (resid 2 through 18 or resid 20...BB297 - 331311 - 345

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Components

#1: Protein Casein kinase II subunit alpha / Casein kinase 2 / CK II 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, CK2A1 / Production host: Escherichia coli (E. coli)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-N4N / 3-[(4-pyridin-2-yl-1,3-thiazol-2-yl)amino]benzoic acid


Mass: 297.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H11N3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 3.05 Å3/Da / Density % sol: 59.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: reservoir composition: 30 % (w/v) PEG8000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate, pH 6.5; crystallization drop composition before equilibration: 0.01 ml reservoir solution plus 0. ...Details: reservoir composition: 30 % (w/v) PEG8000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate, pH 6.5; crystallization drop composition before equilibration: 0.01 ml reservoir solution plus 0.02 ml enzyme stock solution (6 mg/ml enzyme, 0.5 M NaCl, 25 mM Tris/HCl, pH 8.5); the 2-aminothiazole-type inhibitor 17 was introduced by extensive soaking

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9202 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 1.756→89.148 Å / Num. obs: 68306 / % possible obs: 66.5 % / Redundancy: 17.4 % / Biso Wilson estimate: 34.62 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.019 / Rrim(I) all: 0.08 / Rsym value: 0.077 / Net I/σ(I): 21.2
Reflection shellResolution: 1.756→1.796 Å / Redundancy: 15.5 % / Rmerge(I) obs: 1.822 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3417 / CC1/2: 0.662 / Rpim(I) all: 0.475 / Rrim(I) all: 1.884 / Rsym value: 1.822 / % possible all: 12.2

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Processing

Software
NameVersionClassification
XDSdata reduction
autoPROCdata scaling
PHASERphasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HME

6hme


Resolution: 1.756→57.19 Å / SU ML: 0.1826 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.2362
RfactorNum. reflection% reflectionSelection details
Rfree0.2044 1360 1.99 %1360
Rwork0.1817 ---
obs0.1822 68305 63.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.58 Å2
Refinement stepCycle: LAST / Resolution: 1.756→57.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5597 0 57 385 6039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00515844
X-RAY DIFFRACTIONf_angle_d0.77947911
X-RAY DIFFRACTIONf_chiral_restr0.0513811
X-RAY DIFFRACTIONf_plane_restr0.00481022
X-RAY DIFFRACTIONf_dihedral_angle_d22.96942202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.756-1.80.363930.3021172X-RAY DIFFRACTION1.66
1.8-1.870.2712180.2924812X-RAY DIFFRACTION7.89
1.87-1.950.3166440.26982258X-RAY DIFFRACTION21.83
1.95-2.060.2582850.23224030X-RAY DIFFRACTION38.86
2.06-2.180.25371450.22256897X-RAY DIFFRACTION66.57
2.18-2.350.25012080.214110301X-RAY DIFFRACTION99.03
2.35-2.590.22312060.202710447X-RAY DIFFRACTION99.99
2.59-2.960.2242190.196310497X-RAY DIFFRACTION99.99
2.96-3.730.20362150.172110562X-RAY DIFFRACTION99.99
3.74-57.190.17642170.163110969X-RAY DIFFRACTION99.87
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)
12.62274362585-0.7245802684190.827686096940.986841438352-0.5452924232241.357761598950.06840124149430.0381230035918-0.128898506575-0.119980653546-0.063956518087-0.05024124323960.1062933357240.1689156278343.6766622901E-50.2813626857790.008962319828680.03246469767570.284380513318-0.01624561106910.2402255411762.21019065315-48.881664183215.6290577774
20.659894390953-0.764683522107-0.355169226431.457467803740.8988595629020.7811025657-0.532972757608-0.547782796304-0.2245797388110.6850247254950.2156373521050.3304249997090.5050913285740.0167177731698-0.02654362973180.462592285670.126240273435-0.03114853632520.556081431115-0.05898281970360.3582466590322.3239728612-39.280467355131.1933988752
31.73033384277-0.946284295344-0.233369043171.644799926190.305693530792.23611314553-0.108768441725-0.2731520278450.05734222217770.1207839306370.1693341225240.0122368448780.0630333208403-0.1386149290010.006232866125190.2134824443450.03083549136920.002058372215590.305138373268-0.007103702059780.233637704583-17.1332203707-38.374126493326.1439377276
40.7867274921610.7332451766330.7664581233652.673853788990.4249868876381.68597264227-0.1033699175450.120234394980.0658933542157-0.1371983091630.0599286074441-0.105870105612-0.2466520542130.04672768598470.0006563603775880.130373756391-0.01889494397870.05030557521660.211759206945-0.05663725307210.180025470003-14.9835748188-60.73641792444.7524617366
50.1515111400560.1451433765-0.08512823996730.134548336864-0.08000693418430.04519157569290.294798337654-0.8061327707190.1962638107450.629496860464-0.4839521780060.220526876577-0.1657920685190.261658850385-0.001186233166110.573835267155-0.1204021388390.0882564657410.644935657808-0.1156942963820.435790215039-23.1709587858-61.099846372161.5561009193
61.838845356640.75804366416-0.5191323567511.93285563185-0.2147738891212.167458731460.122748296323-0.327013078738-0.01002612794190.212237343580.01646593055920.003564749798940.1043516200440.117859539580.01610999381880.171693613485-0.0367946058298-0.01992774360760.319186653595-0.04696162260950.217363502147-24.9231914112-79.7463752555.9986079388
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 108 )
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 332 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 108 )
5X-RAY DIFFRACTION5chain 'B' and (resid 109 through 129 )
6X-RAY DIFFRACTION6chain 'B' and (resid 130 through 333 )

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