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Yorodumi- PDB-2dls: Solution structure of the PDZ domain of human Rho guanine nucleot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dls | ||||||
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Title | Solution structure of the PDZ domain of human Rho guanine nucleotide exchange factor 11 | ||||||
Components | Rho guanine nucleotide exchange factor 11 | ||||||
Keywords | SIGNALING PROTEIN / PDZ domain / Rho guanine nucleotide exchange factor 11 / PDZ-RhoGEF / ARHGEF11 / KIAA0380 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information Sema4D induced cell migration and growth-cone collapse / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / establishment of cell polarity / NRAGE signals death through JNK / RHOC GTPase cycle / CDC42 GTPase cycle / Rho protein signal transduction / RHOA GTPase cycle / striated muscle contraction ...Sema4D induced cell migration and growth-cone collapse / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / establishment of cell polarity / NRAGE signals death through JNK / RHOC GTPase cycle / CDC42 GTPase cycle / Rho protein signal transduction / RHOA GTPase cycle / striated muscle contraction / RAC1 GTPase cycle / GTPase activator activity / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / regulation of cell growth / G alpha (12/13) signalling events / actin cytoskeleton organization / G protein-coupled receptor signaling pathway / positive regulation of DNA-templated transcription / nucleoplasm / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Inoue, K. / Suetake, T. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the PDZ domain of human Rho guanine nucleotide exchange factor 11 Authors: Inoue, K. / Suetake, T. / Hayashi, F. / 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 | 2dls.cif.gz | 514.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dls.ent.gz | 448.5 KB | Display | PDB format |
PDBx/mmJSON format | 2dls.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/2dls ftp://data.pdbj.org/pub/pdb/validation_reports/dl/2dls | 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: 9441.792 Da / Num. of mol.: 1 / Fragment: PDZ domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: ARHGEF11, KIAA0380 / Plasmid: P050919-12 / Production host: Cell free synthesis / References: UniProt: O15085 |
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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: 1.20mM U-15N, 13C-labeled protein; 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: 7.0 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / 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: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |