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Yorodumi- PDB-2dky: Solution structure of the SAM-domain of Rho-GTPase-activating pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dky | ||||||
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Title | Solution structure of the SAM-domain of Rho-GTPase-activating protein 7 | ||||||
Components | Rho-GTPase-activating protein 7 | ||||||
Keywords | SIGNALING PROTEIN / CELL-FREE PROTEIN SYNTHESIS / PROTEIN REGULATION / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information hindbrain morphogenesis / negative regulation of focal adhesion assembly / regulation of Rho protein signal transduction / focal adhesion assembly / regulation of small GTPase mediated signal transduction / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / RHOB GTPase cycle / cortical actin cytoskeleton / RHOC GTPase cycle ...hindbrain morphogenesis / negative regulation of focal adhesion assembly / regulation of Rho protein signal transduction / focal adhesion assembly / regulation of small GTPase mediated signal transduction / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / RHOB GTPase cycle / cortical actin cytoskeleton / RHOC GTPase cycle / positive regulation of execution phase of apoptosis / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOA GTPase cycle / heart morphogenesis / : / forebrain development / RAC1 GTPase cycle / GTPase activator activity / SH2 domain binding / negative regulation of cell migration / caveola / neural tube closure / regulation of actin cytoskeleton organization / ruffle membrane / activation of cysteine-type endopeptidase activity involved in apoptotic process / regulation of cell shape / actin cytoskeleton organization / membrane raft / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / focal adhesion / lipid binding / apoptotic process / signal transduction / endoplasmic reticulum / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Goroncy, A.K. / Sato, M. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the SAM-domain of Rho-GTPase-activating protein 7 Authors: Goroncy, A.K. / Sato, M. / Koshiba, S. / Inoue, M. / 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 | 2dky.cif.gz | 556.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dky.ent.gz | 467.5 KB | Display | PDB format |
PDBx/mmJSON format | 2dky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dky_validation.pdf.gz | 342.4 KB | Display | wwPDB validaton report |
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Full document | 2dky_full_validation.pdf.gz | 466.9 KB | Display | |
Data in XML | 2dky_validation.xml.gz | 32.3 KB | Display | |
Data in CIF | 2dky_validation.cif.gz | 49.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/2dky ftp://data.pdbj.org/pub/pdb/validation_reports/dk/2dky | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10199.683 Da / Num. of mol.: 1 / Fragment: SAM-domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: CELL-FREE PROTEIN SYNTHESIS / Gene: DLC1, ARHGAP7, KIAA1723, STARD12 / Plasmid: P050207-01 / References: UniProt: Q96QB1 |
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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: 1.08mM SAM DOMAIN, 20mM d-TRIS-HCL, 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 | 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 / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |