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- PDB-2a5d: Structural basis for the activation of cholera toxin by human ARF6-GTP -
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Open data
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Basic information
Entry | Database: PDB / ID: 2a5d | ||||||
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Title | Structural basis for the activation of cholera toxin by human ARF6-GTP | ||||||
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![]() | PROTEIN TRANSPORT/TRANSFERASE / PROTEIN TRANSPORT-TRANSFERASE complex | ||||||
Function / homology | ![]() erythrocyte apoptotic process / protein localization to cleavage furrow / maintenance of postsynaptic density structure / positive regulation of mitotic cytokinetic process / regulation of dendritic spine development / galactose binding / establishment of epithelial cell polarity / protein localization to endosome / negative regulation of protein localization to cell surface / negative regulation of dendrite development ...erythrocyte apoptotic process / protein localization to cleavage furrow / maintenance of postsynaptic density structure / positive regulation of mitotic cytokinetic process / regulation of dendritic spine development / galactose binding / 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 / glycosyltransferase activity / hepatocyte apoptotic process / cleavage furrow / regulation of presynapse assembly / synaptic vesicle endocytosis / Transferases; Glycosyltransferases; Pentosyltransferases / catalytic complex / endocytic vesicle / localization / signaling adaptor activity / vesicle-mediated transport / positive regulation of tyrosine phosphorylation of STAT protein / ruffle / nucleotidyltransferase activity / 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 / toxin activity / early endosome membrane / midbody / postsynapse / periplasmic space / cell differentiation / cell adhesion / endosome / cell cycle / cell division / focal adhesion / GTPase activity / glutamatergic synapse / lipid binding / GTP binding / Golgi apparatus / extracellular space / extracellular exosome / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | O'Neal, C.J. / Jobling, M.G. / Holmes, R.K. / Hol, W.G.J. | ||||||
![]() | ![]() Title: Structural basis for the activation of cholera toxin by human ARF6-GTP. Authors: O'Neal, C.J. / Jobling, M.G. / Holmes, R.K. / Hol, W.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.8 KB | Display | ![]() |
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PDB format | ![]() | 68.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 811.6 KB | Display | ![]() |
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Full document | ![]() | 815 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 16.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2a5fC ![]() 2a5gC ![]() 1o3yS ![]() 1s5eS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is the heterodimer present in the asymmetric unit. |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 20110.166 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 21710.779 Da / Num. of mol.: 1 / Fragment: A1 subunit / Mutation: E110D, E112D, C187S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P01555, NAD+-diphthamide ADP-ribosyltransferase |
-Non-polymers , 5 types, 295 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MG / |
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#4: Chemical | ChemComp-GTP / |
#5: Chemical | ChemComp-NA / |
#6: Chemical | ChemComp-GOL / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG2000mme, cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2004 |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 36064 / Num. obs: 36064 / % possible obs: 93.3 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 56.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1. mouse ARF1 (1O3Y) 2. CTA1 (1S5E) Resolution: 1.8→45.74 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 5.246 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.063 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→45.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.797→1.844 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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