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- PDB-4rll: Crystal structure of human CK2alpha in complex with the ATP-compe... -

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Basic information

Entry
Database: PDB / ID: 4rll
TitleCrystal structure of human CK2alpha in complex with the ATP-competitive inhibitor 4-[(E)-(fluoren-9-ylidenehydrazinylidene)-methyl] benzoate
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE / 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 / Maturation of hRSV A proteins / Sin3-type complex ...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 / Maturation of hRSV A proteins / Sin3-type complex / 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 / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / kinase activity / KEAP1-NFE2L2 pathway / rhythmic process / 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 / 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 / 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-E91 / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGuerra, B. / Rasmussen, T.D.L. / Schnitzler, A. / Jensen, H.H. / Boldyreff, B.S. / Miyata, Y. / Marcussen, N. / Niefind, K. / Issinger, O.G.
CitationJournal: Cancer Lett / Year: 2015
Title: Protein kinase CK2 inhibition is associated with the destabilization of HIF-1 alpha in human cancer cells.
Authors: Guerra, B. / Rasmussen, T.D. / Schnitzler, A. / Jensen, H.H. / Boldyreff, B.S. / Miyata, Y. / Marcussen, N. / Niefind, K. / Issinger, O.G.
History
DepositionOct 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4853
Polymers40,0671
Non-polymers4182
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.490, 45.450, 64.010
Angle α, β, γ (deg.)90.00, 111.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 40066.742 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-335)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CK2A1, CSNK2A1 / Plasmid: pt7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-E91 / 4-[(E)-(9H-fluoren-9-ylidenehydrazinylidene)methyl]benzoic acid


Mass: 326.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H14N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 1.98 Å3/Da / Density % sol: 37.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Reservoir: 30 % PEG 4000, 0.2 M ammonium acetate, 0.1 M sodium citrate pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 19, 2012
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 26413 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 25.03 Å2 / Rmerge(I) obs: 0.0707 / Rsym value: 0.0788 / Net I/σ(I): 15.94
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.85-1.955.350.7272.2337790.72796.5
1.95-2.075.150.4343.7636540.43497.3
2.07-2.254.810.2526.0941160.25297
2.25-2.55.250.1591039610.15998.2
2.5-2.95.380.09715.9738650.09798.1
2.9-3.35.240.05526.2522260.05598.1
3.3-3.94.810.03537.118730.03598.7
3.9-5.44.870.02447.5218090.02499.1
5.4-505.320.02551.7411300.02597.8

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PVR

2pvr


Resolution: 1.85→36.141 Å / SU ML: 0.21 / σ(F): 1.37 / Phase error: 21.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2133 1345 5.09 %RANDOM
Rwork0.1697 ---
obs0.1719 26409 97.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→36.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 31 216 3026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042947
X-RAY DIFFRACTIONf_angle_d0.7853993
X-RAY DIFFRACTIONf_dihedral_angle_d11.751115
X-RAY DIFFRACTIONf_chiral_restr0.032410
X-RAY DIFFRACTIONf_plane_restr0.004515
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.85-1.91610.30081270.26182457245797
1.9161-1.99280.29481090.22992474247497
1.9928-2.08350.21891500.20532443244397
2.0835-2.19340.23891570.18292459245998
2.1934-2.33080.24011480.18262463246397
2.3308-2.51070.22121230.17482538253898
2.5107-2.76330.22691370.18012508250898
2.7633-3.16290.2311290.17692531253198
3.1629-3.98410.2071330.14332554255499
3.9841-36.14780.16691320.14822637263799
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)
13.9082-2.16630.12292.081-0.56490.8382-0.0897-0.3088-0.7432-0.0190.1990.54360.2255-0.3257-0.08280.2465-0.0776-0.02910.33930.03810.3354-14.1506-2.823847.8245
25.2906-1.4753-4.18368.62893.29018.75310.0416-0.2573-0.0727-0.0081-0.2002-0.2590.1757-0.0630.1460.14940.0353-0.0420.43790.12260.3002-24.384613.909743.9559
36.97290.76272.35190.98970.87431.6079-0.19220.04410.2354-0.20240.220.4212-0.1833-0.169-0.04850.23880.0114-0.00780.30370.07510.2817-17.221110.480347.3924
41.40430.22530.1752.70540.35171.75390.0173-0.0859-0.0104-0.07290.0120.2226-0.0654-0.1288-0.02370.17150.0155-0.00320.19910.02770.1747-2.89528.523345.5024
52.82322.76012.50256.21493.91874.3185-0.35120.24190.3165-0.627-0.13450.5571-0.8188-0.15950.4320.30570.0191-0.02540.18370.01410.16915.740114.453431.5287
62.4292.3694-1.017.6637-2.48010.8577-0.05590.1597-0.1024-0.34340.027-0.04820.19610.15020.03710.24240.05510.01980.228-0.02840.156313.5582.809529.0759
71.0580.56190.484.65721.45372.39880.0437-0.0980.013-0.04040.0608-0.2488-0.08970.2166-0.09090.11470.00590.00850.1971-0.00150.164910.745413.649.0361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 74 )
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 129 )
4X-RAY DIFFRACTION4chain 'A' and (resid 130 through 227 )
5X-RAY DIFFRACTION5chain 'A' and (resid 228 through 249 )
6X-RAY DIFFRACTION6chain 'A' and (resid 250 through 280 )
7X-RAY DIFFRACTION7chain 'A' and (resid 281 through 329 )

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