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- PDB-6hbn: HIGH-SALT STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOF... -

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Basic information

Entry
Database: PDB / ID: 6hbn
TitleHIGH-SALT STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA/CSKN2A1 GENE PRODUCT) IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR THN27
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2 / catalytic subunit CK2alpha / CSNK2A1
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 / Sin3-type complex / Maturation of hRSV A proteins ...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 / Sin3-type complex / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of signal transduction by p53 class mediator / 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 / Regulation of PTEN stability and activity / Wnt signaling pathway / KEAP1-NFE2L2 pathway / positive regulation of protein catabolic process / rhythmic process / kinase activity / 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 / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / DNA damage response / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / 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-FXB / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsNiefind, K. / Hochscherf, J. / Dimper, V. / Witulski, B. / 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
DepositionAug 10, 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 17, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)81,22817
Polymers80,1332
Non-polymers1,09415
Water11,584643
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6028
Polymers40,0671
Non-polymers5367
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6259
Polymers40,0671
Non-polymers5598
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.550, 71.620, 128.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Casein kinase II subunit alpha / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: 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: obtained synthetically / Formula: C21H21NO3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 643 / 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: 2.06 Å3/Da / Density % sol: 40.35 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 90 MIKROLITER ENZYME STOCK SOLUTION (6 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 10 MIKROLITER INHIBITOR STOCK SOLUTION (10 MM INHIBITOR IN DMSO). THIS MIXTURE WAS ...Details: 90 MIKROLITER ENZYME STOCK SOLUTION (6 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 10 MIKROLITER INHIBITOR STOCK SOLUTION (10 MM INHIBITOR IN DMSO). THIS MIXTURE WAS INCUBATED FOR 30 MIN AT ROOM TEMPERATURE. THE RESERVOIR SOLUTION OF THE CRYSTALLIZATION EXPERIMENT WAS 4.4 M NACL, 0.1 M CITRIC ACID, PH 5.5. PRIOR TO EQUILIBRATION THE CRYSTALLIZATION DROP WAS COMPOSED OF 1 MIKROLITER RESERVOIR SOLUTION PLUS 1 MIKROLITER ENZYME/INHIBITOR MIXTURE.,VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.59→64.016 Å / Num. obs: 88883 / % possible obs: 99.79 % / Redundancy: 6.2 % / Biso Wilson estimate: 24.73 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08839 / Rpim(I) all: 0.03889 / Rrim(I) all: 0.09679 / Rsym value: 0.08839 / Net I/σ(I): 10.2
Reflection shellResolution: 1.59→1.647 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.361 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 8769 / CC1/2: 0.835 / Rpim(I) all: 0.6071 / Rrim(I) all: 1.493 / Rsym value: 1.361 / % possible all: 99.83

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Processing

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

5cqu


Resolution: 1.59→64.015 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.19
RfactorNum. reflection% reflection
Rfree0.2172 1778 2 %
Rwork0.187 --
obs0.1876 88882 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.59→64.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5622 0 63 643 6328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065895
X-RAY DIFFRACTIONf_angle_d0.8067990
X-RAY DIFFRACTIONf_dihedral_angle_d12.7013522
X-RAY DIFFRACTIONf_chiral_restr0.053819
X-RAY DIFFRACTIONf_plane_restr0.0051031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.63290.31911350.2886634X-RAY DIFFRACTION100
1.6329-1.6810.29171350.2576590X-RAY DIFFRACTION100
1.681-1.73530.2531360.24876663X-RAY DIFFRACTION100
1.7353-1.79730.28161360.23416660X-RAY DIFFRACTION100
1.7973-1.86930.25161340.21376584X-RAY DIFFRACTION100
1.8693-1.95430.22651360.20046690X-RAY DIFFRACTION100
1.9543-2.05740.23251360.1876647X-RAY DIFFRACTION100
2.0574-2.18630.22971370.17876688X-RAY DIFFRACTION100
2.1863-2.35510.21251370.17676719X-RAY DIFFRACTION100
2.3551-2.59210.21621360.18886690X-RAY DIFFRACTION100
2.5921-2.96720.21021380.19346759X-RAY DIFFRACTION100
2.9672-3.73830.20151380.17546728X-RAY DIFFRACTION99
3.7383-64.06690.20211440.17277052X-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)
10.7264-0.2726-0.11120.74480.0551.96390.0339-0.0558-0.16410.1420.0488-0.01950.3749-0.20230.00490.2421-0.0014-0.00020.14510.0110.1449-15.305815.8006-12.2732
20.46260.56920.29061.1553-0.10911.2406-0.04180.06990.29520.2054-0.1107-0.28250.1808-0.1724-0.00060.3636-0.0578-0.03510.37410.00940.3207-26.602613.1754-27.8463
31.39760.05920.19880.1370.19040.68340.10740.0269-0.4113-0.1136-0.05290.00370.6405-0.21520.01480.3601-0.0745-0.05240.2252-0.01290.29-22.051413.1599-18.1263
40.6750.1421-0.67551.74530.47321.32110.01170.29830.1636-0.35310.04570.3083-0.0713-0.34020.00090.22810.0036-0.05880.2670.02640.2815-15.362429.3286-27.5149
50.9085-0.2683-0.85611.31660.32171.9296-0.0467-0.01070.039-0.07020.1213-0.26240.14710.32110.00480.17970.025-0.01450.2235-0.03690.23514.404921.0233-26.7817
61.0233-0.1868-0.232.02740.1571.78490.01560.0380.1782-0.1480.097-0.1774-0.18090.0852-0.00010.2196-0.04420.0360.2128-0.00660.2757-2.97238.0018-28.1452
70.3067-0.3589-0.07710.4353-0.11281.57080.03170.2302-0.0097-0.07520.12430.18320.1203-0.59480.05350.1883-0.012-0.02490.32240.01660.2053-38.128538.5433-19.8896
81.20480.58110.16090.4965-0.32581.2187-0.2870.21160.41540.07990.2234-0.12550.0647-0.2975-0.00030.386-0.049-0.0160.32450.02680.3622-40.931327.6864-4.0003
90.40960.3017-0.46531.4812-0.2890.54160.1022-0.1899-0.10140.12390.03620.04840.3403-0.42940.04560.2528-0.0777-0.0070.35990.04520.2709-36.072533.2334-8.7726
101.2956-0.037-0.29740.74820.72121.92490.0952-0.02120.13180.0039-0.0702-0.039-0.3125-0.26080.01780.19220.05070.01640.1760.03030.1812-29.821752.8219-5.761
111.8748-0.19-0.37140.83980.19951.98420.074-0.06350.14090.1298-0.0113-0.1553-0.21310.1915-0.00020.2987-0.02790.00310.2223-0.0120.2927-15.276950.5715-3.7694
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 74 )
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 113 )
4X-RAY DIFFRACTION4chain 'A' and (resid 114 through 173 )
5X-RAY DIFFRACTION5chain 'A' and (resid 174 through 280 )
6X-RAY DIFFRACTION6chain 'A' and (resid 281 through 335 )
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 44 )
8X-RAY DIFFRACTION8chain 'B' and (resid 45 through 74 )
9X-RAY DIFFRACTION9chain 'B' and (resid 75 through 129 )
10X-RAY DIFFRACTION10chain 'B' and (resid 130 through 280 )
11X-RAY DIFFRACTION11chain 'B' and (resid 281 through 335 )

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