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Open data
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Basic information
Entry | Database: PDB / ID: 1jwh | ||||||
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Title | Crystal Structure of Human Protein Kinase CK2 Holoenzyme | ||||||
![]() | (Casein kinase ...) x 2 | ||||||
![]() | TRANSFERASE / casein kinase 2 / CK2 holoenzyme / protein kinase CK2 | ||||||
Function / homology | ![]() regulation of DNA binding / adiponectin-activated signaling pathway / positive regulation of activin receptor signaling pathway / UTP-C complex / endothelial tube morphogenesis / negative regulation of viral life cycle / regulation of transcription by RNA polymerase III / protein kinase regulator activity / regulation of chromosome separation / positive regulation of aggrephagy ...regulation of DNA binding / adiponectin-activated signaling pathway / positive regulation of activin receptor signaling pathway / UTP-C complex / endothelial tube morphogenesis / negative regulation of viral life cycle / regulation of transcription by RNA polymerase III / protein kinase regulator activity / 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 / Maturation of hRSV A proteins / positive regulation of SMAD protein signal transduction / negative regulation of apoptotic signaling pathway / negative regulation of blood vessel endothelial cell migration / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / rhythmic process / protein-macromolecule adaptor activity / kinase activity / positive regulation of cell growth / protein-containing complex assembly / peptidyl-serine phosphorylation / secretory granule lumen / Regulation of TP53 Activity through Phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / ficolin-1-rich granule lumen / protein stabilization / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / cell cycle / protein domain specific binding / negative regulation of cell population proliferation / protein phosphorylation / protein serine kinase activity / signaling receptor binding / protein serine/threonine kinase activity / apoptotic process / DNA damage response / chromatin binding / positive regulation of cell population proliferation / Neutrophil degranulation / chromatin / signal transduction / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Niefind, K. / Guerra, B. / Ermakowa, I. / Issinger, O.G. | ||||||
![]() | ![]() 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. #1: ![]() Title: Crystallization and Preliminary Characterization of Crystals of Human Protein Kinase CK2 Authors: Niefind, K. / Guerra, B. / Ermakowa, I. / Issinger, O.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 244.4 KB | Display | ![]() |
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PDB format | ![]() | 194.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 783.2 KB | Display | ![]() |
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Full document | ![]() | 873.1 KB | Display | |
Data in XML | ![]() | 54.6 KB | Display | |
Data in CIF | ![]() | 74.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1dawS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The asymmetric unit contains one complete CK2 tetramer comprising two catalytic and two regulatory subunits. |
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Components
-Casein kinase ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 40240.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 24969.412 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 219 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-ANP / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.8 % Description: WHILE THE OVERALL DATA COMPLETENESS FOR THE GIVEN RESOLUTION RANGE (59.3 A - 3.1 A) WAS 98.4 % ONLY 78.7 % OF ALL POSSIBLE DATA WERE USED IN REFINEMENT WITH CNS. THE REASON FOR THIS ...Description: WHILE THE OVERALL DATA COMPLETENESS FOR THE GIVEN RESOLUTION RANGE (59.3 A - 3.1 A) WAS 98.4 % ONLY 78.7 % OF ALL POSSIBLE DATA WERE USED IN REFINEMENT WITH CNS. THE REASON FOR THIS DISCREPANCY WAS THAT THE DATA HAD NOT BEEN WILSON SCALED AFTER PROCESSING AND ALL NEGATIVE INTENSITIES HAD BEEN SET TO ZERO WHEN THE INTENSITIES HAD BEEN CONVERTED TO STRUCTURE AMPLITUDES. ALL THESE ZERO DATA WERE IGNORED DURING REFINEMENT WITH CNS. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 9.3 Details: initial composition of the drop: 3 ul rhCK2 stock solution [5 mg/ml enzyme in 25 mM Tris/HCl, 300 mM NaCl, 1 mM dithiothreitole, pH 8.5], 1.5 ul reservoir solution [20 % (w/v) PEG3350, 200 ...Details: initial composition of the drop: 3 ul rhCK2 stock solution [5 mg/ml enzyme in 25 mM Tris/HCl, 300 mM NaCl, 1 mM dithiothreitole, pH 8.5], 1.5 ul reservoir solution [20 % (w/v) PEG3350, 200 mM dipotassium hydrogenphosphate], 3 ul 1 mM adenylyl imidodiphosphate (AMPPNP), 3 ul 2 mM magnesium chloride, 2 ul 10 % (w/v) polyethylene glycol 400 dodecylether (Thesit), pH 9.3, VAPOR DIFFUSION, SITTING DROP, temperature 285K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 12 ℃ / pH: 8.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 26, 2000 |
Radiation | Monochromator: silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8428 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→59.3 Å / Num. obs: 29935 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 92.2 Å2 / Limit h max: 49 / Limit h min: 0 / Limit k max: 48 / Limit k min: 0 / Limit l max: 30 / Limit l min: 0 / Observed criterion F max: 2867098.76 / Observed criterion F min: 1.5 / Rsym value: 0.096 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 3.1→3.2 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.6 / Rsym value: 42 / % possible all: 90.4 |
Reflection | *PLUS Num. measured all: 268848 / Rmerge(I) obs: 0.096 |
Reflection shell | *PLUS % possible obs: 90.4 % / Rmerge(I) obs: 0.42 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: POLY-ALANINE BACKBONE OF CK2A FROM ZEA MAYS (PDB ENTRY 1DAW) Resolution: 3.1→59.3 Å / Rfactor Rfree error: 0.011 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 27.2984 Å2 / ksol: 0.269435 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 243.39 Å2 / Biso mean: 90.96 Å2 / Biso min: 3.08 Å2
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Refine Biso |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→59.3 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 60 Å / σ(F): 0 / % reflection Rfree: 4 % / Rfactor obs: 0.267 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.458 / % reflection Rfree: 2.2 % / Rfactor Rwork: 0.458 |