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- PDB-6hmd: STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALP... -

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Basic information

Entry
Database: PDB / ID: 6hmd
TitleSTRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 gene product) IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR AR18
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2 / catalytic subunit ck2alpha' / csnk2a2 / indeno[1 / 2-b]indole-type inhibitor
Function / homology
Function and homology information


regulation of mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins ...regulation of mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins / negative regulation of apoptotic signaling pathway / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / acrosomal vesicle / Signal transduction by L1 / liver regeneration / cerebral cortex development / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / chromatin / nucleoplasm / ATP binding / nucleus / 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-GDW / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5145
Polymers43,0181
Non-polymers4964
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-5 kcal/mol
Surface area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.890, 45.820, 48.520
Angle α, β, γ (deg.)113.02, 89.21, 91.18
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 43018.012 Da / Num. of mol.: 1 / 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
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GDW / 5-[2-(diethylamino)ethyl]-7,8-dihydro-6~{H}-indeno[1,2-b]indole-9,10-dione


Mass: 336.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N2O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 180 MICROLITER ENZYME STOCK SOLUTION (6 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WAS MIXED and incubated WITH 20 MIKROLITER of a STOCK SOLUTION of the inhibitor 4B0 (10 MM 4B0 IN DMSO). ...Details: 180 MICROLITER ENZYME STOCK SOLUTION (6 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WAS MIXED and incubated WITH 20 MIKROLITER of a STOCK SOLUTION of the inhibitor 4B0 (10 MM 4B0 IN DMSO). 20 MICROLITERS OF the resulting solution WAS MIXED WITH 10 MICROLITERS OF RESERVOIR SOLUTION (700 MM LICL, 28 % (W/V) PEG 6000, 100 MM TRIS/HCL, PH 8.5) IN EACH WELL OF A CRYSTALLIZATION PLATE. A SINGLE MACROSEED, grown UNDER THE SAME CONDITIONS, WAS ADDED TO EACH DROPLET of the plate. THE DROPLETS WERE EQUILIBRATED AT 293.15 K using the sitting drop variant of the VAPOR DIFFUSION method. This procedure generated large single crystals of a CK2alpha'/4B0 complex. Afterwards, the inhibitor 4B0 was exchanged against AR18 by an extensive soaking procedure of several steps.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.920042 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920042 Å / Relative weight: 1
ReflectionResolution: 1→44.88 Å / Num. obs: 177359 / % possible obs: 92.18 % / Redundancy: 3.9 % / Biso Wilson estimate: 10.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04708 / Rpim(I) all: 0.02787 / Rrim(I) all: 0.05476 / Rsym value: 0.04708 / Net I/σ(I): 15.67
Reflection shellResolution: 1→1.036 Å / Redundancy: 4 % / Rmerge(I) obs: 1.028 / Mean I/σ(I) obs: 1.36 / Num. unique obs: 17032 / CC1/2: 0.557 / Rpim(I) all: 0.5973 / Rrim(I) all: 1.189 / Rsym value: 1.028 / % possible all: 88.55

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
Arcimboldophasing
ARP/wARPmodel building
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1→22.327 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 18.05
RfactorNum. reflection% reflection
Rfree0.1718 1773 1 %
Rwork0.1493 --
obs0.1496 177317 92.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1→22.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 34 482 3284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0223053
X-RAY DIFFRACTIONf_angle_d1.3174149
X-RAY DIFFRACTIONf_dihedral_angle_d22.4971185
X-RAY DIFFRACTIONf_chiral_restr0.073424
X-RAY DIFFRACTIONf_plane_restr0.006538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.0270.31341310.273612953X-RAY DIFFRACTION89
1.027-1.05720.2031320.233613083X-RAY DIFFRACTION89
1.0572-1.09130.211330.200913198X-RAY DIFFRACTION90
1.0913-1.13040.1891340.183313234X-RAY DIFFRACTION90
1.1304-1.17560.19791350.170913381X-RAY DIFFRACTION91
1.1756-1.22910.18181360.162113426X-RAY DIFFRACTION92
1.2291-1.29390.17591370.152613547X-RAY DIFFRACTION93
1.2939-1.3750.16831380.147113669X-RAY DIFFRACTION93
1.375-1.48110.17331390.137213772X-RAY DIFFRACTION94
1.4811-1.63010.14531400.133313871X-RAY DIFFRACTION95
1.6301-1.86590.15521400.132213882X-RAY DIFFRACTION95
1.8659-2.35040.14721420.132814048X-RAY DIFFRACTION96
2.3504-22.33260.17871360.14613480X-RAY DIFFRACTION92

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