+Open data
-Basic information
Entry | Database: PDB / ID: 1e0s | ||||||
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Title | small G protein Arf6-GDP | ||||||
Components | ADP-ribosylation factor 6 | ||||||
Keywords | G PROTEIN / RAS / ARF / ARF6 / MEMBRANE TRAFFIC | ||||||
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 / endocytic recycling / MET receptor recycling / thioesterase binding / 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 / synaptic vesicle endocytosis / regulation of presynapse assembly / endocytic vesicle / signaling adaptor activity / vesicle-mediated transport / ruffle / positive regulation of protein localization to plasma membrane / 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 / intracellular protein transport / positive regulation of neuron projection development / recycling endosome membrane / GDP binding / Clathrin-mediated endocytosis / early endosome membrane / presynapse / nervous system development / cell cortex / midbody / postsynapse / endosome / cell differentiation / cell adhesion / cell division / focal adhesion / GTPase activity / glutamatergic synapse / GTP binding / Golgi apparatus / extracellular exosome / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Menetrey, J. / Cherfils, J. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2000 Title: Structure of Arf6-Gdp Suggests a Basis for Guanine Nucleotide Exchange Factors Specificity Authors: Menetrey, J. / Macia, E. / Pasqualato, S. / Franco, M. / Cherfils, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e0s.cif.gz | 53 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e0s.ent.gz | 36.5 KB | Display | PDB format |
PDBx/mmJSON format | 1e0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e0s_validation.pdf.gz | 781.5 KB | Display | wwPDB validaton report |
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Full document | 1e0s_full_validation.pdf.gz | 783.3 KB | Display | |
Data in XML | 1e0s_validation.xml.gz | 10 KB | Display | |
Data in CIF | 1e0s_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/1e0s ftp://data.pdbj.org/pub/pdb/validation_reports/e0/1e0s | HTTPS FTP |
-Related structure data
Related structure data | 1hurS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19978.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARF6 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P62330 |
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#2: Chemical | ChemComp-GDP / |
#3: Chemical | ChemComp-BME / |
#4: Chemical | ChemComp-NH4 / |
#5: Water | ChemComp-HOH / |
Sequence details | ELECTRON DENSITY CONNECTED TO CYS 155 WAS MODELLED AS A TRUNCATED DTT MOLECULE ELECTRON DENSITY ...ELECTRON DENSITY CONNECTED TO CYS 155 WAS MODELLED AS A TRUNCATED DTT MOLECULE ELECTRON DENSITY NEAR GDP PHOSPHATE WAS MODELLED AS NH4+ LYS: THE C-TERMINAL RESIDUE WAS NOT SEEN IN THE DENSITY MAPS LYS55 LIES OUTSIDE THE FAVOURED RAMACHANDR |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 37 % | ||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: 2M AMMONIUM SULFATE, 0.1M TRIS/HCL PH 8.5 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.963 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.963 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→30 Å / Num. obs: 8748 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 20.7 Å2 / Rsym value: 0.064 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.28→2.36 Å / Redundancy: 5.5 % / Rsym value: 0.152 / % possible all: 98.5 |
Reflection | *PLUS Num. measured all: 76362 / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 98.5 % / Rmerge(I) obs: 0.152 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HUR Resolution: 2.28→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 17.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→30 Å
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Refine LS restraints |
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