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Yorodumi- PDB-2da9: Solution structure of the third SH3 domain of SH3-domain kinase b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2da9 | ||||||
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Title | Solution structure of the third SH3 domain of SH3-domain kinase binding protein 1 (Regulator of ubiquitous kinase, Ruk) | ||||||
Components | SH3-domain kinase binding protein 1 | ||||||
Keywords | APOPTOSIS / SH3 domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information Reelin signalling pathway / Negative regulation of MET activity / EGFR downregulation / ubiquitin-dependent endocytosis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of B cell activation / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / endocytic vesicle / cytoskeleton organization ...Reelin signalling pathway / Negative regulation of MET activity / EGFR downregulation / ubiquitin-dependent endocytosis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of B cell activation / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / endocytic vesicle / cytoskeleton organization / actin filament organization / cytoplasmic vesicle membrane / SH3 domain binding / cell-cell junction / cell migration / regulation of cell shape / molecular adaptor activity / cytoskeleton / neuron projection / focal adhesion / apoptotic process / ubiquitin protein ligase binding / synapse Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, restrained molecular dynamics | ||||||
Authors | Ohnishi, S. / Kigawa, T. / Saito, K. / Koshiba, S. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the third SH3 domain of SH3-domain kinase binding protein 1 (Regulator of ubiquitous kinase, Ruk) Authors: Ohnishi, S. / Kigawa, T. / Saito, K. / Koshiba, S. / Inoue, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2da9.cif.gz | 400.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2da9.ent.gz | 337.5 KB | Display | PDB format |
PDBx/mmJSON format | 2da9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2da9_validation.pdf.gz | 340.7 KB | Display | wwPDB validaton report |
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Full document | 2da9_full_validation.pdf.gz | 470.8 KB | Display | |
Data in XML | 2da9_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 2da9_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/2da9 ftp://data.pdbj.org/pub/pdb/validation_reports/da/2da9 | 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: 7603.343 Da / Num. of mol.: 1 / Fragment: The third SH3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: Sh3kbp1 / Plasmid: P050425-21 / References: UniProt: Q8R550 |
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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: 1.0mM protein U-15N, 13C; 20mM d-Tris-HCl (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, restrained molecular dynamics Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |