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- PDB-6hme: LOW-SALT STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFO... -

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Basic information

Entry
Database: PDB / ID: 6hme
TitleLOW-SALT STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA; CSNK2A1 gene product) IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR THN27
ComponentsCasein kinase II subunit alphaCasein kinase 2
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2 / catalytic subunit CK2alpha / CSNK2A1 / indenoindole-type 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 / Maturation of hRSV A proteins / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC ...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 / Maturation of hRSV A proteins / 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 / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / 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 / KEAP1-NFE2L2 pathway / double-strand break repair / rhythmic process / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / protein stabilization / non-specific serine/threonine protein kinase / regulation of cell cycle / 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-FXB / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNiefind, K. / Lindenblatt, D. / Jose, J. / Le Borgne, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationDFG NI 643/4-2 Germany
Citation
Journal: Acs Omega / Year: 2019
Title: Diacritic Binding of an Indenoindole Inhibitor by CK2 alpha Paralogs Explored by a Reliable Path to Atomic Resolution CK2 alpha ' 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.
#1: Journal: Pharmaceuticals (Basel) / Year: 2017
Title: Unexpected Binding Mode of a Potent Indeno[1,2-b]indole-Type Inhibitor of Protein Kinase CK2 Revealed by Complex Structures with the Catalytic Subunit CK2alpha and Its Paralog CK2alpha'
Authors: Hochscherf, J. / Lindenblatt, D. / Witulski, B. / Birus, R. / Aichele, D. / Marminon, C. / Bouaziz, Z. / Le Borgne, M. / Jose, J. / Niefind, K.
#2: Journal: J. Mol. Biol. / Year: 2003
Title: Crystal structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit.
Authors: Ermakova, I. / Boldyreff, B. / Issinger, O.G. / Niefind, K.
History
DepositionSep 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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)85,43322
Polymers83,3712
Non-polymers2,06220
Water7,008389
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,72311
Polymers41,6851
Non-polymers1,03710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,71011
Polymers41,6851
Non-polymers1,02510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.370, 126.370, 124.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 6 types, 409 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: SO4
#5: Chemical ChemComp-FXB / 5-propan-2-yl-4-prop-2-enoxy-7,8-dihydro-6~{H}-indeno[1,2-b]indole-9,10-dione


Mass: 335.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C21H21NO3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O

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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: 3.11 Å3/Da / Density % sol: 60.39 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 180 MICROLITERS OF ENZYME SOLUTION (6 MG/ML CK2ALPHA, 0.025 M TRIS/HCL, PH 8.5, 0.5 M NACL) WERE MIXED WITH 20 MICROLITERS OF INHIBITOR STOCK SOLUTION (0.010 M INHIBITOR THN27 IN DMSO). THIS ...Details: 180 MICROLITERS OF ENZYME SOLUTION (6 MG/ML CK2ALPHA, 0.025 M TRIS/HCL, PH 8.5, 0.5 M NACL) WERE MIXED WITH 20 MICROLITERS OF INHIBITOR STOCK SOLUTION (0.010 M INHIBITOR THN27 IN DMSO). THIS MIXTURE WAS INCUBATED FOR 30 MIN AT ROOM TEMPERATURE. THE RESERVOIR SOLUTION OF THE CRYSTALLIZATION EXPERIMENT WAS 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE TRIHYDRATE, PH 6.5, 30% (W/V) PEG 8,000. PRIOR TO EQUILIBRATION THE CRYSTALLIZATION DROP WAS COMPOSED OF 10 MICROLITERS RESERVOIR SOLUTION PLUS 20 MICROLITERS ENZYME/INHIBITOR MIXTURE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.85→89.357 Å / Num. obs: 86172 / % possible obs: 99.82 % / Redundancy: 6.5 % / Biso Wilson estimate: 40.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05501 / Rpim(I) all: 0.02339 / Rrim(I) all: 0.05994 / Rsym value: 0.05501 / Net I/σ(I): 16.12
Reflection shellResolution: 1.85→1.916 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.701 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 8521 / CC1/2: 0.535 / Rpim(I) all: 0.7053 / Rrim(I) all: 1.843 / Rsym value: 1.701 / % possible all: 99.88

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ONI

5oni


Resolution: 1.85→89.357 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.197 1724 2 %
Rwork0.1749 --
obs0.1754 86126 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→89.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5608 0 126 389 6123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065902
X-RAY DIFFRACTIONf_angle_d0.8357987
X-RAY DIFFRACTIONf_dihedral_angle_d16.333501
X-RAY DIFFRACTIONf_chiral_restr0.054811
X-RAY DIFFRACTIONf_plane_restr0.0051019
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8499-1.90440.37171420.33936939X-RAY DIFFRACTION100
1.9044-1.96590.28721420.2946952X-RAY DIFFRACTION100
1.9659-2.03610.26631420.23646959X-RAY DIFFRACTION100
2.0361-2.11770.25241420.21656946X-RAY DIFFRACTION100
2.1177-2.2140.25561420.19886951X-RAY DIFFRACTION100
2.214-2.33080.20391420.17956976X-RAY DIFFRACTION100
2.3308-2.47680.20521430.17747024X-RAY DIFFRACTION100
2.4768-2.66810.19851430.18037001X-RAY DIFFRACTION100
2.6681-2.93660.22331440.18547039X-RAY DIFFRACTION100
2.9366-3.36150.21771450.17437080X-RAY DIFFRACTION100
3.3615-4.23520.16841450.15417136X-RAY DIFFRACTION100
4.2352-89.46150.16971520.15967399X-RAY DIFFRACTION99
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)
10.9769-1.1225-0.69354.8231.71872.2124-0.0823-0.1615-0.05190.00590.1048-0.07440.13290.0389-0.04110.349-0.0033-0.00040.41460.02410.378347.1048-0.988947.2473
22.6961-2.21391.62184.8695-1.23271.95050.39610.4866-0.1321-0.8455-0.36110.02260.22040.19160.01520.46610.01580.00210.4218-0.00290.386838.5174-0.323336.8464
31.7304-0.64170.25682.0884-0.30772.35230.14820.08790.128-0.4157-0.07390.0364-0.1158-0.0323-0.06030.45090.06620.02880.3366-0.01480.358438.653517.95436.082
45.1779-0.1452-1.17052.31160.43721.94780.1429-0.7640.05740.2796-0.0141-0.0255-0.05970.2278-0.1350.474-0.098-0.0850.4337-0.02030.364476.896621.859327.7224
53.06040.4822.35991.9429-0.42486.0598-0.07650.0658-0.07810.0443-0.10890.06130.1192-0.31290.19340.46310.0098-0.00870.4242-0.01840.460253.328811.065613.0281
63.86623.03460.84173.01791.20785.04950.0123-0.01520.03030.1872-0.26750.009-0.0066-0.10620.24040.37890.0003-0.01370.28590.0010.384156.80313.004316.0166
72.86781.5046-1.57532.344-0.72661.461-0.1560.42140.1941-0.26220.1860.2449-0.0404-0.2926-0.0350.4364-0.0063-0.08670.34340.01730.373362.418523.77657.902
82.40760.3821-0.74671.5191-0.35621.87920.02790.2501-0.3005-0.2510.0257-0.03330.19950.068-0.05060.4901-0.0571-0.07380.3367-0.03330.425777.928918.71537.673
93.20430.32590.72824.707-1.69766.01520.07330.0537-0.4777-0.3119-0.1637-0.91760.31430.7870.11660.47980.01840.01750.4822-0.06420.611895.019117.04466.4391
102.84180.10890.29873.9016-0.73583.7633-0.00860.20790.4133-0.20660.05940.1847-0.482-0.0022-0.0680.5136-0.1131-0.02730.3610.02740.431578.874434.90763.3162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 96 )
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 149 )
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 333 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 24 )
5X-RAY DIFFRACTION5chain 'B' and (resid 25 through 58 )
6X-RAY DIFFRACTION6chain 'B' and (resid 59 through 87 )
7X-RAY DIFFRACTION7chain 'B' and (resid 88 through 168 )
8X-RAY DIFFRACTION8chain 'B' and (resid 169 through 249 )
9X-RAY DIFFRACTION9chain 'B' and (resid 250 through 280 )
10X-RAY DIFFRACTION10chain 'B' and (resid 281 through 333 )

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