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Yorodumi- PDB-1wi0: Solution structure of the PB1 domain of mouse mitogen activated p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wi0 | ||||||
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Title | Solution structure of the PB1 domain of mouse mitogen activated protein kinase kinase 5 (MAP2K5) | ||||||
Components | Mitogen activated protein kinase kinase 5 | ||||||
Keywords | TRANSFERASE / PB1 domain / protein-protein interaction site / cytoplasmic signalling / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information ERK5 cascade / negative regulation of chemokine (C-X-C motif) ligand 2 production / : / negative regulation of response to cytokine stimulus / negative regulation of heterotypic cell-cell adhesion / negative regulation of interleukin-8 production / mitogen-activated protein kinase kinase / negative regulation of cell migration involved in sprouting angiogenesis / negative regulation of NF-kappaB transcription factor activity / MAP kinase kinase activity ...ERK5 cascade / negative regulation of chemokine (C-X-C motif) ligand 2 production / : / negative regulation of response to cytokine stimulus / negative regulation of heterotypic cell-cell adhesion / negative regulation of interleukin-8 production / mitogen-activated protein kinase kinase / negative regulation of cell migration involved in sprouting angiogenesis / negative regulation of NF-kappaB transcription factor activity / MAP kinase kinase activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of protein metabolic process / positive regulation of epithelial cell proliferation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / cellular response to growth factor stimulus / spindle / MAPK cascade / heart development / positive regulation of cell growth / protein tyrosine kinase activity / protein kinase activity / protein phosphorylation / protein serine/threonine kinase activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Yoneyama, M. / Hayashi, F. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the PB1 domain of mouse mitogen activated protein kinase kinase 5 (MAP2K5) Authors: Yoneyama, M. / Hayashi, F. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wi0.cif.gz | 664.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wi0.ent.gz | 554.2 KB | Display | PDB format |
PDBx/mmJSON format | 1wi0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wi0_validation.pdf.gz | 344.5 KB | Display | wwPDB validaton report |
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Full document | 1wi0_full_validation.pdf.gz | 511 KB | Display | |
Data in XML | 1wi0_validation.xml.gz | 46.5 KB | Display | |
Data in CIF | 1wi0_validation.cif.gz | 68.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/1wi0 ftp://data.pdbj.org/pub/pdb/validation_reports/wi/1wi0 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 12408.806 Da / Num. of mol.: 1 / Fragment: PB1 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA A230106F01 / Plasmid: P031125-28 References: UniProt: Q9WVS7, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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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: 1mM PB1 domain U-15N, 13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 297 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |