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- PDB-5ooi: STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALP... -

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Basic information

Entry
Database: PDB / ID: 5ooi
TitleSTRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA') IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR 4P
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2 / indenoindole-type inhibitors
Function / homology
Function and homology information


regulation of mitophagy / regulation of chromosome separation / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Synthesis of PC / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...regulation of mitophagy / regulation of chromosome separation / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Synthesis of PC / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of apoptotic signaling pathway / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / acrosomal vesicle / liver regeneration / Signal transduction by L1 / cerebral cortex development / Wnt signaling pathway / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / spermatogenesis / 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 / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / chromatin / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-9YE / ACETATE ION / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsHochscherf, J. / Lindenblatt, D. / Witulski, B. / Birus, R. / Aichele, D. / Marminon, C. / Bouaziz, Z. / Le Borgne, M. / Jose, J. / Niefind, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationNI 643/4-2 Germany
Citation
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 CK2 alpha and Its Paralog CK2 alpha '.
Authors: Hochscherf, J. / Lindenblatt, D. / Witulski, B. / Birus, R. / Aichele, D. / Marminon, C. / Bouaziz, Z. / Le Borgne, M. / Jose, J. / Niefind, K.
#1: Journal: J. Mol. Biol. / Year: 2011
Title: Structure of the human protein kinase CK2 catalytic subunit CK2alpha' and interaction thermodynamics with the regulatory subunit CK2beta
Authors: Bischoff, N. / Olsen, B. / Raaf, J. / Bretner, M. / Issinger, O.G. / Niefind, K.
#2: Journal: Bioorg. Med. Chem. / Year: 2012
Title: Indeno[1,2-b]indole derivatives as a novel class of potent human protein kinase CK2 inhibitors.
Authors: Hundsdoerfer, C. / Hemmerling, H.J. / Goetz, C. / Totzke, F. / Bednarski, P. / Le Borgne, M. / Jose, J.
History
DepositionAug 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 2.0Oct 3, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 3.0Oct 10, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 3.1Jan 17, 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)86,93212
Polymers85,7602
Non-polymers1,17210
Water7,981443
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A: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5718
Polymers42,8801
Non-polymers6917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3614
Polymers42,8801
Non-polymers4823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.488, 112.128, 143.692
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 42879.867 Da / Num. of mol.: 2 / Mutation: C336S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A2, CK2A2 / Production host: Escherichia coli (E. coli)
References: UniProt: P19784, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 453 molecules

#2: Chemical ChemComp-9YE / 4-(3-methylbut-2-enoxy)-5-propan-2-yl-7,8-dihydro-6~{H}-indeno[1,2-b]indole-9,10-dione


Mass: 363.450 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H25NO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 90 MIKROLITER ENZYME STOCK SOLUTION (5 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 10 MIKROLITER 4P STOCK SOLUTION (10 MM 4P IN DMSO). THIS MIXTURE WAS INCUBATED FOR 30 MIN ...Details: 90 MIKROLITER ENZYME STOCK SOLUTION (5 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 10 MIKROLITER 4P STOCK SOLUTION (10 MM 4P IN DMSO). THIS MIXTURE WAS INCUBATED FOR 30 MIN AT ROOM TEMPERATURE. THE RESERVOIR SOLUTION OF THE CRYSTALLIZATION EXPERIMENT WAS 25 % (W/ V) PEG3350, 0.2 M AMMONIUM ACETATE, 0.1 M HEPES BUFFER, PH 8.5. PRIOR TO EQUILIBRATION THE CRYSTALLIZATION DROP WAS COMPOSED OF 1 MIKROLITER RESERVOIR SOLUTION PLUS 1 MIKROLITER ENZYME/4P MIXTURE., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.998→71.48 Å / Num. obs: 51742 / % possible obs: 99.69 % / Redundancy: 6.7 % / Biso Wilson estimate: 24.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.177 / Rsym value: 0.177 / Net I/σ(I): 7.39
Reflection shellResolution: 1.998→2.07 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.191 / Mean I/σ(I) obs: 1.41 / Num. unique obs: 4979 / CC1/2: 0.673 / Rsym value: 1.191 / % possible all: 97.59

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OFM

3ofm


Resolution: 1.998→71.48 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / Phase error: 23.24
RfactorNum. reflection% reflection
Rfree0.2211 1041 2.01 %
Rwork0.1738 --
obs0.1748 51726 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.998→71.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5513 0 83 443 6039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115748
X-RAY DIFFRACTIONf_angle_d1.1247759
X-RAY DIFFRACTIONf_dihedral_angle_d14.5223542
X-RAY DIFFRACTIONf_chiral_restr0.067795
X-RAY DIFFRACTIONf_plane_restr0.008994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9982-2.10360.28341490.2227030X-RAY DIFFRACTION98
2.1036-2.23540.25321380.21057139X-RAY DIFFRACTION100
2.2354-2.4080.29021160.19537214X-RAY DIFFRACTION100
2.408-2.65030.25731530.18287183X-RAY DIFFRACTION100
2.6503-3.03380.23681560.1757256X-RAY DIFFRACTION100
3.0338-3.82220.19631750.15697269X-RAY DIFFRACTION100
3.8222-71.89240.18721540.15837594X-RAY DIFFRACTION100
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)
12.23230.1180.25420.74120.3761.3097-0.0843-0.14960.43760.01150.0562-0.0568-0.3003-0.01690.00440.1930.00120.01270.1723-0.03930.1796-13.5621.02317.6079
21.3788-0.1498-0.09630.83880.12030.50050.0522-0.5728-0.24240.1644-0.0053-0.04710.0497-0.04580.01970.1362-0.0030.01010.23890.01860.1118-22.3793-14.73813.5303
31.3167-0.3291-0.12511.9852-0.54521.53540.0635-0.1804-0.62520.1075-0.00220.07450.184-0.3406-0.05090.1918-0.0607-0.00780.23730.060.3089-30.7448-24.46019.388
42.9854-0.55170.81343.1852-0.11626.6036-0.0320.5018-0.2413-0.2926-0.1479-0.3661-0.02630.63150.00290.1565-0.02610.02480.198-0.0880.1981-19.6671-18.3-3.5278
52.83211.5991-0.87184.4094-0.62491.9472-0.132-0.1541-0.6132-0.14490.0078-0.16960.37920.12270.14350.23940.04740.00370.340.00890.3291-14.8673-22.737545.0024
61.4722-0.4785-0.13241.09660.28411.4167-0.0606-0.0527-0.25070.0437-0.01770.02980.1303-0.06840.07150.1535-0.02340.02650.2788-0.02040.1755-28.0893-9.631944.4613
72.05560.23850.25480.95050.81522.0486-0.0467-0.07210.1034-0.0240.01330.0126-0.3531-0.1016-0.08350.20960.02780.01740.2642-0.06110.1936-33.25723.962942.2091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 174 )
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 250 )
3X-RAY DIFFRACTION3chain 'A' and (resid 251 through 305 )
4X-RAY DIFFRACTION4chain 'A' and (resid 306 through 333 )
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 109 )
6X-RAY DIFFRACTION6chain 'B' and (resid 110 through 250 )
7X-RAY DIFFRACTION7chain 'B' and (resid 251 through 333 )

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