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Yorodumi- PDB-2bau: Solution NMR structure of the micelle-bound myristoylated N-termi... -
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-Basic information
Entry | Database: PDB / ID: 2bau | ||||||
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Title | Solution NMR structure of the micelle-bound myristoylated N-terminal Arf6 | ||||||
Components | ADP-ribosylation factor 6 | ||||||
Keywords | SIGNALING PROTEIN / Micelle-bound / myristoylated peptide | ||||||
Function / homology | Function and homology information erythrocyte apoptotic process / protein localization to cleavage furrow / maintenance of postsynaptic density structure / positive regulation of mitotic cytokinetic process / regulation of dendritic spine development / establishment of epithelial cell polarity / protein localization to endosome / negative regulation of protein localization to cell surface / negative regulation of dendrite development / negative regulation of receptor-mediated endocytosis ...erythrocyte apoptotic process / protein localization to cleavage furrow / maintenance of postsynaptic density structure / positive regulation of mitotic cytokinetic process / regulation of dendritic spine development / establishment of epithelial cell polarity / protein localization to endosome / negative regulation of protein localization to cell surface / negative regulation of dendrite development / negative regulation of receptor-mediated endocytosis / regulation of Rac protein signal transduction / ruffle assembly / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / regulation of filopodium assembly / MET receptor recycling / thioesterase binding / endocytic recycling / filopodium membrane / Flemming body / protein localization to cell surface / TBC/RABGAPs / cortical actin cytoskeleton organization / positive regulation of actin filament polymerization / hepatocyte apoptotic process / cleavage furrow / regulation of presynapse assembly / synaptic vesicle endocytosis / endocytic vesicle / signaling adaptor activity / vesicle-mediated transport / ruffle / small monomeric GTPase / cellular response to nerve growth factor stimulus / G protein activity / liver development / protein localization to plasma membrane / positive regulation of protein secretion / positive regulation of protein localization to plasma membrane / intracellular protein transport / positive regulation of neuron projection development / recycling endosome membrane / GDP binding / presynapse / Clathrin-mediated endocytosis / nervous system development / cell cortex / early endosome membrane / midbody / postsynapse / cell differentiation / cell adhesion / endosome / cell cycle / cell division / focal adhesion / GTPase activity / glutamatergic synapse / GTP binding / Golgi apparatus / extracellular exosome / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Gizachew, D. | ||||||
Citation | Journal: Febs Lett. / Year: 2006 Title: NMR structural studies of the myristoylated N-terminus of ADP ribosylation factor 6 (Arf6). Authors: Gizachew, D. / Oswald, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bau.cif.gz | 47.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bau.ent.gz | 35.4 KB | Display | PDB format |
PDBx/mmJSON format | 2bau.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bau_validation.pdf.gz | 361.8 KB | Display | wwPDB validaton report |
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Full document | 2bau_full_validation.pdf.gz | 430.3 KB | Display | |
Data in XML | 2bau_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 2bau_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/2bau ftp://data.pdbj.org/pub/pdb/validation_reports/ba/2bau | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 1064.279 Da / Num. of mol.: 1 / Fragment: N-terminal peptide / Source method: obtained synthetically Details: This sequence is the N-terminal peptide of a protein which occurs naturally in Homo sapiens (human). References: UniProt: P62330 |
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#2: Chemical | ChemComp-MYR / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 5mM Myristoylated N-terminal Arf6; 5mM acetate buffer, 100mM fully deuterated dodecylphosphocholine (DPC) Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 7 / pH: 5 / 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: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz |
-Processing
NMR software | Name: X-PLOR / Version: NIH-2.9.9 / Developer: Lakowski / Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 12 |