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Yorodumi- PDB-1ujy: Solution structure of SH3 domain in Rac/Cdc42 guanine nucleotide ... -
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-Basic information
Entry | Database: PDB / ID: 1ujy | ||||||
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Title | Solution structure of SH3 domain in Rac/Cdc42 guanine nucleotide exchange factor(GEF) 6 | ||||||
Components | Rho guanine nucleotide exchange factor 6 | ||||||
Keywords | SIGNALING PROTEIN / structural genomics / SH3 domain / GEF 6 / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / lamellipodium assembly / NRAGE signals death through JNK / CDC42 GTPase cycle / RHOU GTPase cycle / JNK cascade / RAC1 GTPase cycle / GTPase activator activity / guanyl-nucleotide exchange factor activity / G beta:gamma signalling through CDC42 ...Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / lamellipodium assembly / NRAGE signals death through JNK / CDC42 GTPase cycle / RHOU GTPase cycle / JNK cascade / RAC1 GTPase cycle / GTPase activator activity / guanyl-nucleotide exchange factor activity / G beta:gamma signalling through CDC42 / G alpha (12/13) signalling events / cell-cell junction / lamellipodium / apoptotic process / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | He, F. / Muto, Y. / Uda, H. / Koshiba, S. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. ...He, F. / Muto, Y. / Uda, H. / Koshiba, S. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Kobayashi, N. / Tanaka, A. / Osanai, T. / Matsuo, Y. / Ohara, O. / Nagase, T. / Kikuno, R. / Nagayama, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of SH3 domain in Rac/Cdc42 guanine nucleotide exchange factor(GEF) 6 Authors: He, F. / Muto, Y. / Uda, H. / Koshiba, S. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Kobayashi, N. / ...Authors: He, F. / Muto, Y. / Uda, H. / Koshiba, S. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Kobayashi, N. / Tanaka, A. / Osanai, T. / Matsuo, Y. / Ohara, O. / Nagase, T. / Kikuno, R. / Nagayama, M. / Yokoyama, S. | ||||||
History |
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Remark 650 | HELIX determination method: author determined |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ujy.cif.gz | 446 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ujy.ent.gz | 372.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ujy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/1ujy ftp://data.pdbj.org/pub/pdb/validation_reports/uj/1ujy | 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: 8365.116 Da / Num. of mol.: 1 / Fragment: SH3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell free protein synthesis / Gene: KAZUSA ha01154 / Plasmid: P021021-16 / References: UniProt: Q15052 |
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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: 0.8mM SH3 U-15N, 13C; 20mM phosphate buffer NA; 100mM NaCl; 0.02% NaN3; 90%H2O, 10%D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / 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, structures with the lowest energy, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |