[English] 日本語
Yorodumi- PDB-1wxu: Solution structure of the SH3 domain of mouse peroxisomal biogene... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wxu | ||||||
---|---|---|---|---|---|---|---|
Title | Solution structure of the SH3 domain of mouse peroxisomal biogenesis factor 13 | ||||||
Components | peroxisomal biogenesis factor 13 | ||||||
Keywords | PROTEIN TRANSPORT / SH3 domain / PEX13 / protein-protein interaction / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses | ||||||
Function / homology | Function and homology information Class I peroxisomal membrane protein import / microtubule-based peroxisome localization / : / peroxisome targeting sequence binding / E3 ubiquitin ligases ubiquitinate target proteins / peroxisomal importomer complex / protein import into peroxisome matrix, docking / fatty acid alpha-oxidation / Peroxisomal protein import / peroxisomal membrane ...Class I peroxisomal membrane protein import / microtubule-based peroxisome localization / : / peroxisome targeting sequence binding / E3 ubiquitin ligases ubiquitinate target proteins / peroxisomal importomer complex / protein import into peroxisome matrix, docking / fatty acid alpha-oxidation / Peroxisomal protein import / peroxisomal membrane / suckling behavior / cerebral cortex cell migration / locomotory behavior / neuron migration / peroxisome / intracellular membrane-bounded organelle Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Yoneyama, M. / Sato, M. / 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 SH3 domain of mouse peroxisomal biogenesis factor 13 Authors: Yoneyama, M. / Sato, M. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1wxu.cif.gz | 535.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1wxu.ent.gz | 449.9 KB | Display | PDB format |
PDBx/mmJSON format | 1wxu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wxu_validation.pdf.gz | 342.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1wxu_full_validation.pdf.gz | 475.6 KB | Display | |
Data in XML | 1wxu_validation.xml.gz | 31.9 KB | Display | |
Data in CIF | 1wxu_validation.cif.gz | 49.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/1wxu ftp://data.pdbj.org/pub/pdb/validation_reports/wx/1wxu | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 9920.976 Da / Num. of mol.: 1 / Fragment: SH3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: Pex13 / Plasmid: P040802-03 / References: UniProt: Q8CCJ5, UniProt: Q9D0K1*PLUS |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 1.09mM SH3 domain U-15N, 13C; 20mM d-Tris-HCl; 200mM NaCl; 1mM d-DTT; 0.02% NaN3; 10%D2O Solvent system: 90% H2O/10% D2O |
---|---|
Sample conditions | Ionic strength: 220 / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 Conformers calculated total number: 100 / Conformers submitted total number: 20 |