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Yorodumi- PDB-2ee5: Solution structure of the N-teruminus extended RhoGAP domain from... -
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-Basic information
Entry | Database: PDB / ID: 2ee5 | ||||||
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Title | Solution structure of the N-teruminus extended RhoGAP domain from human Rho GTPase activating protein 5 variant | ||||||
Components | Rho GTPase activating protein 5 variant | ||||||
Keywords | HYDROLASE / all alpha protein / GTPase-activating protein for Rho family members / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information epithelial cell migration / mammary gland development / RHOF GTPase cycle / RHOD GTPase cycle / regulation of small GTPase mediated signal transduction / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of mesenchymal cell proliferation / regulation of cell size ...epithelial cell migration / mammary gland development / RHOF GTPase cycle / RHOD GTPase cycle / regulation of small GTPase mediated signal transduction / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of mesenchymal cell proliferation / regulation of cell size / RHOB GTPase cycle / positive regulation of epithelial cell migration / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / Rho protein signal transduction / RHOG GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / RAC1 GTPase cycle / GTPase activator activity / SH2 domain binding / cell adhesion / GTPase activity / endoplasmic reticulum / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, restrained molecular dynamics | ||||||
Authors | Tomizawa, T. / Tochio, N. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the N-teruminus extended RhoGAP domain from human Rho GTPase activating protein 5 variant Authors: Tomizawa, T. / Tochio, N. / Koshiba, S. / Watanabe, S. / Harada, T. / 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 | 2ee5.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2ee5.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 2ee5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/2ee5 ftp://data.pdbj.org/pub/pdb/validation_reports/ee/2ee5 | HTTPS FTP |
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-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: 25186.547 Da / Num. of mol.: 1 / Fragment: RhoGAP domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Plasmid: P060123-15 References: UniProt: Q59ER0, UniProt: Q13017*PLUS, small monomeric GTPase |
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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: 1.31mM RhoGAP domain U-15N, 13C; 20mM d-Tris-HCl(pH 7.0); 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 / Pressure: ambient / Temperature: 296 K |
-NMR measurement
NMR spectrometer |
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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: structures with the least restraint violations, structures with the lowest energy, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |