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Yorodumi- PDB-1v5u: Solution Structure of the C-terminal Pleckstrin Homology Domain o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v5u | ||||||
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Title | Solution Structure of the C-terminal Pleckstrin Homology Domain of Sbf1 from Mouse | ||||||
Components | SET binding factor 1 | ||||||
Keywords | SIGNALING PROTEIN / Sbf1 / MTMR5 / the Pleckstrin Homology domain / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information Synthesis of PIPs at the ER membrane / pseudophosphatase activity / guanyl-nucleotide exchange factor activity => GO:0005085 / RAB GEFs exchange GTP for GDP on RABs / regulation of GTPase activity / regulation of cell growth / spermatogenesis / nuclear body / perinuclear region of cytoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Li, H. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution Structure of the C-terminal Pleckstrin Homology Domain of Sbf1 from Mouse Authors: Li, H. / 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 | 1v5u.cif.gz | 706.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v5u.ent.gz | 590 KB | Display | PDB format |
PDBx/mmJSON format | 1v5u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1v5u_validation.pdf.gz | 344.2 KB | Display | wwPDB validaton report |
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Full document | 1v5u_full_validation.pdf.gz | 514.1 KB | Display | |
Data in XML | 1v5u_validation.xml.gz | 43.6 KB | Display | |
Data in CIF | 1v5u_validation.cif.gz | 66.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/1v5u ftp://data.pdbj.org/pub/pdb/validation_reports/v5/1v5u | HTTPS FTP |
-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: 13058.756 Da / Num. of mol.: 1 / Fragment: The Pleckstrin Homology Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA 2610510A08 / Plasmid: P030212-74 / References: GenBank: 26344980, UniProt: Q6ZPE2*PLUS |
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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: 0.28mM Pleckstrin Homology domain U-13C, 15N; 20mM PiNa(6.0); 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: 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: 600 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,target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |