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Yorodumi- PDB-4rll: Crystal structure of human CK2alpha in complex with the ATP-compe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rll | ||||||
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Title | Crystal structure of human CK2alpha in complex with the ATP-competitive inhibitor 4-[(E)-(fluoren-9-ylidenehydrazinylidene)-methyl] benzoate | ||||||
Components | Casein kinase II subunit alphaCasein kinase 2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / 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 / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / peptidyl-threonine phosphorylation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of protein catabolic process / rhythmic process / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / protein stabilization / regulation of cell cycle / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / positive regulation of cell population proliferation / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Guerra, B. / Rasmussen, T.D.L. / Schnitzler, A. / Jensen, H.H. / Boldyreff, B.S. / Miyata, Y. / Marcussen, N. / Niefind, K. / Issinger, O.G. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rll.cif.gz | 159.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rll.ent.gz | 126.1 KB | Display | PDB format |
PDBx/mmJSON format | 4rll.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rl/4rll ftp://data.pdbj.org/pub/pdb/validation_reports/rl/4rll | HTTPS FTP |
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-Related structure data
Related structure data | 4rlkC 2pvrS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-E91 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.79 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 19, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PVR Resolution: 1.85→36.141 Å / SU ML: 0.21 / σ(F): 1.37 / Phase error: 21.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→36.141 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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