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Yorodumi- PDB-2ed1: Solution structure of the SH3 domain of 130 kDa phosphatidylinosi... -
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-Basic information
Entry | Database: PDB / ID: 2ed1 | ||||||
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Title | Solution structure of the SH3 domain of 130 kDa phosphatidylinositol 4,5-biphosphate-dependent ARF1 GTPase-activating protein | ||||||
Components | 130 kDa phosphatidylinositol 4,5-biphosphate-dependent ARF1 GTPase-activating protein | ||||||
Keywords | SIGNALING PROTEIN / GTPase activation / Membrane / Metal-binding / SH3 domain / Zinc-finger / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information positive regulation of membrane tubulation / negative regulation of dendritic spine development / VxPx cargo-targeting to cilium / protein localization to cilium / podosome / regulation of postsynapse organization / phosphatidylserine binding / phosphatidylinositol-3,4,5-trisphosphate binding / cilium assembly / phosphatidylinositol-4,5-bisphosphate binding ...positive regulation of membrane tubulation / negative regulation of dendritic spine development / VxPx cargo-targeting to cilium / protein localization to cilium / podosome / regulation of postsynapse organization / phosphatidylserine binding / phosphatidylinositol-3,4,5-trisphosphate binding / cilium assembly / phosphatidylinositol-4,5-bisphosphate binding / GTPase activator activity / trans-Golgi network membrane / dendritic spine / cadherin binding / Golgi membrane / glutamatergic synapse / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Abe, H. / Tochio, N. / Miyamoto, K. / Saito, K. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the SH3 domain of 130 kDa phosphatidylinositol 4,5-biphosphate-dependent ARF1 GTPase-activating protein Authors: Abe, H. / Tochio, N. / Miyamoto, K. / Saito, K. / 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 | 2ed1.cif.gz | 436.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ed1.ent.gz | 366.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ed1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/2ed1 ftp://data.pdbj.org/pub/pdb/validation_reports/ed/2ed1 | 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: 8302.002 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: DDEF1 / Plasmid: P050627-26 / References: UniProt: Q9ULH1 |
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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: 1.15mM Protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 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: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |