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- PDB-3lvq: The crystal structure of ASAP3 in complex with Arf6 in transition... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3lvq | ||||||
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Title | The crystal structure of ASAP3 in complex with Arf6 in transition state | ||||||
![]() | Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3, ADP-ribosylation factor 6 | ||||||
![]() | PROTEIN TRANSPORT / Arf / GAP / GDP / ASAP3 / UPLC1 / Arf6 / ArfGAP / Linkers / Alternative splicing / ANK repeat / Coiled coil / Cytoplasm / Metal-binding / Phosphoprotein / Polymorphism / Zinc / Zinc-finger / Cell membrane / Endosome / ER-Golgi transport / Golgi apparatus / GTP-binding / Lipoprotein / Myristate / Nucleotide-binding / Transport | ||||||
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 / 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 / regulation of stress fiber assembly / 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 / GTPase activator activity / small monomeric GTPase / cellular response to nerve growth factor stimulus / G protein activity / positive regulation of GTPase 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 / cell migration / Clathrin-mediated endocytosis / presynapse / nervous system development / cell cortex / midbody / early endosome membrane / postsynapse / cell differentiation / cell adhesion / endosome / cell division / intracellular membrane-bounded organelle / focal adhesion / GTPase activity / glutamatergic synapse / GTP binding / Golgi apparatus / extracellular exosome / nucleoplasm / membrane / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ismail, S.A. / Vetter, I.R. / Sot, B. / Wittinghofer, A. | ||||||
![]() | ![]() Title: The structure of an Arf-ArfGAP complex reveals a Ca2+ regulatory mechanism Authors: Ismail, S.A. / Vetter, I.R. / Sot, B. / Wittinghofer, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.3 KB | Display | ![]() |
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PDB format | ![]() | 73.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3lvrC ![]() 2b0oS ![]() 2j5xS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules E
#1: Protein | Mass: 54825.930 Da / Num. of mol.: 1 Fragment: GAP and Ankyrin domain, residues 416-697, residues 11-175 Source method: isolated from a genetically manipulated source Details: Missing the N-terminus amphipathic helix for Arf6 Source: (gene. exp.) ![]() Gene: ASAP3, ARF6 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 10 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/AF3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/AF3.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-GDP / | #5: Chemical | ChemComp-AF3 / | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | NLSSDSSLSS |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 13% PEG 8000, 150mM Magnesium Acetate, 100mM MOPS(pH 7.5), VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 16, 2009 |
Radiation | Monochromator: SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.38→29.42 Å / Num. obs: 8700 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.25 % / Rmerge(I) obs: 0.066 / Rsym value: 0.079 / Net I/σ(I): 22.52 / Num. measured all: 80498 |
Reflection shell | Resolution: 3.38→3.5 Å / Redundancy: 9.45 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 4.94 / Num. unique all: 847 / Rsym value: 0.55 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 2B0o and 2J5X Resolution: 3.38→29.42 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.904 / SU B: 58.227 / SU ML: 0.482 / Cross valid method: THROUGHOUT / ESU R Free: 0.558 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 136.436 Å2
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Refinement step | Cycle: LAST / Resolution: 3.38→29.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.38→3.467 Å / Total num. of bins used: 20
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