[English] 日本語
Yorodumi- PDB-1wxm: Solution Structure of the N-terminal Ras-binding Domain (RBD) in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wxm | ||||||
---|---|---|---|---|---|---|---|
Title | Solution Structure of the N-terminal Ras-binding Domain (RBD) in Human a-Raf Kinase | ||||||
Components | A-Raf proto-oncogene serine/threonine-protein kinase | ||||||
Keywords | TRANSFERASE / Ras-binding domain (RBD) / ubiquitin-like fold / a-Raf kinase / Structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of TOR signaling / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / MAP kinase kinase kinase activity / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / protein modification process / Negative regulation of MAPK pathway ...regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of TOR signaling / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / MAP kinase kinase kinase activity / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / protein modification process / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / MAPK cascade / Signaling by BRAF and RAF1 fusions / positive regulation of peptidyl-serine phosphorylation / Ras protein signal transduction / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / mitochondrion / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Zhao, C. / 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 N-terminal Ras-binding Domain (RBD) in Human a-Raf Kinase Authors: Zhao, C. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. | ||||||
History |
| ||||||
Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1wxm.cif.gz | 501 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1wxm.ent.gz | 417.4 KB | Display | PDB format |
PDBx/mmJSON format | 1wxm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wxm_validation.pdf.gz | 344.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1wxm_full_validation.pdf.gz | 498.4 KB | Display | |
Data in XML | 1wxm_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 1wxm_validation.cif.gz | 53.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/1wxm ftp://data.pdbj.org/pub/pdb/validation_reports/wx/1wxm | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 9125.406 Da / Num. of mol.: 1 / Fragment: Ras-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: ARAF1 / Plasmid: P040712-12 / References: UniProt: P10398, EC: 2.7.1.37 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 0.86mM protein U-15N, 13C; 20mM d-Tris-HCl (pH7.0); 200mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O Solvent system: 90% H2O/10% D2O |
---|---|
Sample conditions | Ionic strength: 200mM / pH: 7.0 / Pressure: ambient / Temperature: 296.0 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function,structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |