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- PDB-3rps: Structure of human CK2alpha in complex with the ATP-competitive i... -

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Basic information

Entry
Database: PDB / ID: 3rps
TitleStructure of human CK2alpha in complex with the ATP-competitive inhibitor 3-(4,5,6,7-tetrabromo-1H-benzotriazol-1-yl)propan-1-ol
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / eukaryotic protein kinase fold / ATP CK2beta / Phosphorylation / cytoplasm nucleus / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 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 / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H2AS121 kinase activity / histone H3S57 kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / histone H3S28 kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / ribosomal protein S6 kinase activity / histone H2AT120 kinase activity / histone H2BS36 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H3S10 kinase activity / AMP-activated protein kinase activity / 3-phosphoinositide-dependent protein kinase activity / histone H3T11 kinase activity / histone H3T3 kinase activity / histone H3T45 kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / KEAP1-NFE2L2 pathway / 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 phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / 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-4B0 / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBischoff, N. / Raaf, J. / Olsen, B. / Bretner, M. / Issinger, O.-G. / Niefind, K.
Citation
Journal: Mol.Cell.Biochem. / Year: 2011
Title: Enzymatic activity with an incomplete catalytic spine - insights from a comparative structural analysis of human CK2alpha and its paralogous isoform CK2alpha'
Authors: Bischoff, N. / Raaf, J. / Olsen, B. / Bretner, M. / Issinger, O.G. / Niefind, K.
#1: Journal: J.Mol.Biol. / Year: 2011
Title: Structure of the human protein kinase CK2 catalytic subunit CK2 and interaction thermodynamics with the regulatory subunit CK2
Authors: Bischoff, N. / Olsen, B. / Raaf, J. / Bretner, M. / Issinger, O.G. / Niefind, K.
#2: Journal: Embo J. / Year: 2001
Title: Crystal structure of human protein kinase CK2: insights into basic properties of the CK2 holoenzyme.
Authors: Niefind, K. / Guerra, B. / Ermakowa, I. / Issinger, O.G.
History
DepositionApr 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 21, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_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)80,9609
Polymers80,1332
Non-polymers8277
Water2,612145
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7265
Polymers40,0671
Non-polymers6604
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)40,2344
Polymers40,0671
Non-polymers1673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.010, 72.010, 133.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 40066.742 Da / Num. of mol.: 2 / Fragment: unp residues 1-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-4B0 / 3-(4,5,6,7-tetrabromo-1H-benzotriazol-1-yl)propan-1-ol


Mass: 492.787 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7Br4N3O
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.88 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.501
11-H, K, -L20.499
ReflectionResolution: 2.3→19.75 Å / Num. all: 30152 / Num. obs: 30062 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.75 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 13.915 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22846 912 3 %RANDOM
Rwork0.17 ---
obs0.1717 29111 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.727 Å2
Baniso -1Baniso -2Baniso -3
1--21.22 Å20 Å20 Å2
2---21.22 Å20 Å2
3---42.43 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5634 0 31 145 5810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225810
X-RAY DIFFRACTIONr_bond_other_d0.0010.024052
X-RAY DIFFRACTIONr_angle_refined_deg0.9211.9517858
X-RAY DIFFRACTIONr_angle_other_deg2.10739754
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0775666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38323.057314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.426151028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3121552
X-RAY DIFFRACTIONr_chiral_restr0.0570.2810
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216406
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021274
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.19763338
X-RAY DIFFRACTIONr_mcbond_other0.20461336
X-RAY DIFFRACTIONr_mcangle_it1.76465422
X-RAY DIFFRACTIONr_scbond_it2.11892472
X-RAY DIFFRACTIONr_scangle_it2.75192436
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.298→2.357 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 69 -
Rwork0.188 2053 -
obs--97.47 %
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)
13.5976-0.32840.03532.1842-1.57583.5442-0.05640.20670.3958-0.1480.0610.1077-0.137-0.2653-0.00450.25680.0220.00390.38110.00640.06119.476-19.944-2.062
21.6252-1.4138-2.07275.74.83976.60440.1184-0.13120.0939-0.16480.0809-0.45680.51160.4413-0.19940.47440.06750.00430.4920.03280.073423.458-40.9244.751
32.35890.03761.41793.8517-0.35774.0270.0359-0.0943-0.13930.2907-0.0202-0.43940.2280.1052-0.01580.37780.0346-0.00620.2499-0.00620.060815.961-26.429-46.675
45.4355-2.0963-4.02322.10471.56515.44380.1824-0.06080.5437-0.08840.08810.0618-0.6542-0.3964-0.27050.51450.0529-0.03390.4705-0.01220.1153-4.908-12.421-53.315
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 12
2X-RAY DIFFRACTION1A117 - 335
3X-RAY DIFFRACTION2A13 - 116
4X-RAY DIFFRACTION3B2 - 12
5X-RAY DIFFRACTION3B117 - 335
6X-RAY DIFFRACTION4B13 - 116

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