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- PDB-4nh1: Crystal structure of a heterotetrameric CK2 holoenzyme complex ca... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4nh1 | ||||||
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Title | Crystal structure of a heterotetrameric CK2 holoenzyme complex carrying the Andante-mutation in CK2beta and consistent with proposed models of autoinhibition and trans-autophosphorylation | ||||||
![]() | (Casein kinase II subunit ...) x 2 | ||||||
![]() | TRANSFERASE / eukaryotic protein kinase fold / phosphotransferase (kinase) / phosphorylation | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Schnitzler, A. / Issinger, O.-G. / Niefind, K. | ||||||
![]() | ![]() Title: The Protein Kinase CK2(Andante) Holoenzyme Structure Supports Proposed Models of Autoregulation and Trans-Autophosphorylation Authors: Schnitzler, A. / Olsen, B.B. / Issinger, O.-G. / Niefind, K. #1: Journal: Mol.Cell.Biochem. / Year: 2005 Title: Biochemical characterization of the recombinant human Drosophila homologues Timekeeper and Andante involved in the Drosophila circadian oscillator. Authors: Rasmussen, T. / Skjth, I.H. / Jensen, H.H. / Niefind, K. / Boldyreff, B. / Issinger, O.G. #2: ![]() 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. #3: Journal: Mol.Cell.Biochem. / Year: 2005 Title: Primary and secondary interactions between CK2alpha and CK2beta lead to ring-like structures in the crystals of the CK2 holoenzyme. Authors: Niefind, K. / 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 | ![]() | 468.7 KB | Display | ![]() |
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PDB format | ![]() | 391.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 941.7 KB | Display | ![]() |
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Full document | ![]() | 957.9 KB | Display | |
Data in XML | ![]() | 39.7 KB | Display | |
Data in CIF | ![]() | 52.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jwhS 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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Components
-Casein kinase II subunit ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 40066.742 Da / Num. of mol.: 2 / Fragment: UNP residues 1-335 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P68400, non-specific serine/threonine protein kinase #2: Protein | Mass: 24951.375 Da / Num. of mol.: 2 / Mutation: Met166Ile Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 29 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.8 % |
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-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Date: Jun 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→46.24 Å / Num. obs: 21878 / Redundancy: 2.4 % / Biso Wilson estimate: 106.58 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 13.85 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JWH Resolution: 3.3→46.237 Å / Occupancy max: 1 / Occupancy min: 0.29 / SU ML: 0.46 / σ(F): 1.35 / Phase error: 29.03 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 308.81 Å2 / Biso mean: 130.8526 Å2 / Biso min: 27.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→46.237 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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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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