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- PDB-2rsv: Solution structure of human full-length vaccinia related kinase 1... -
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Basic information
Entry | Database: PDB / ID: 2rsv | ||||||
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Title | Solution structure of human full-length vaccinia related kinase 1 (VRK1) | ||||||
![]() | Serine/threonine-protein kinase VRK1 | ||||||
![]() | TRANSFERASE / VRK / kinase | ||||||
Function / homology | ![]() Golgi disassembly / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / histone H3S10 kinase activity / kinase activity / histone binding ...Golgi disassembly / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / histone H3S10 kinase activity / kinase activity / histone binding / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / cell division / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / nucleolus / protein kinase binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / torsion angle dynamics, simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
![]() | Koshiba, S. / Tochio, N. / Yokoyama, J. / Kigawa, T. | ||||||
![]() | ![]() Title: A strategy for structure determination of large molecular weight protein using isotope labeling methodology with cell-free protein systhesis: application to 45 kDa human vaccinia related kianse 1 (VRK1) Authors: Koshiba, S. / Tochio, N. / Yokoyama, J. / Yoon, H. / Kigawa, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.2 MB | Display | ![]() |
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PDB format | ![]() | 1.9 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 533.3 KB | Display | ![]() |
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Full document | ![]() | 794.7 KB | Display | |
Data in XML | ![]() | 159.7 KB | Display | |
Data in CIF | ![]() | 201.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 46071.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() References: UniProt: Q99986, non-specific serine/threonine protein kinase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 0.4 MM [U-13C; U-15N; U-2H; 1H ILE, LEU, VAL, ALA METHYL; 1H MET METHYL,GAMMA; 1H PHE EPSILON] VRK1, 20 MM [U-2H] TRIS,100 MM SODIUM CHLORIDE, 50 MM GLUTAMIC ACID, 50 MM ARGININE, 1 MM [U- ...Contents: 0.4 MM [U-13C; U-15N; U-2H; 1H ILE, LEU, VAL, ALA METHYL; 1H MET METHYL,GAMMA; 1H PHE EPSILON] VRK1, 20 MM [U-2H] TRIS,100 MM SODIUM CHLORIDE, 50 MM GLUTAMIC ACID, 50 MM ARGININE, 1 MM [U-2H] DTT, 0.02 % SODIUM AZIDE, 90% H2O/10% D2O; 0.4 MM [U-13C; U-15N; U-2H; 1H ILE, LEU, VAL METHYL; 1H PHE, TYR EPSILON] VRK1, 20 MM [U-2H] TRIS,100 MM SODIUM CHLORIDE, 50 MM GLUTAMIC ACID, 50 MM ARGININE, 1 MM [U-2H] DTT, 0.02 % SODIUM AZIDE, 90% H2O/10% D2O; 0.4 MM [U-15N; U-2H; 13C,1H ILE, LEU, VAL METHYL; 13C,1H PHE DELTA/EPSILON/ZETA] VRK1, 20 MM [U-2H] TRIS,100 MM SODIUM CHLORIDE, 50 MM GLUTAMIC ACID, 50 MM ARGININE, 1 MM [U-2H] DTT, 0.02 % SODIUM AZIDE, 90% H2O/10% D2O; 0.4 MM SAIL-VRK1, 20 MM [U-2H] TRIS, 100 MM SODIUM CHLORIDE, 50 MM GLUTAMIC ACID, 50 MM ARGININE, 1 MM [U-2H] DTT, 0.02 % SODIUM AZIDE, 90% H2O/10% D2O; Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 120 / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz |
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Processing
NMR software |
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Refinement | Method: torsion angle dynamics, simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 18 / Representative conformer: 1 |