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- PDB-1i4t: CRYSTAL STRUCTURE ANALYSIS OF RAC1-GMPPNP IN COMPLEX WITH ARFAPTIN -
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Basic information
Entry | Database: PDB / ID: 1i4t | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF RAC1-GMPPNP IN COMPLEX WITH ARFAPTIN | ||||||
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![]() | SIGNALING PROTEIN / complex / coiled coil / G-protein | ||||||
Function / homology | ![]() membrane curvature sensor activity / Retrograde transport at the Trans-Golgi-Network / regulation of respiratory burst / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / GTP-dependent protein binding / negative regulation of receptor-mediated endocytosis ...membrane curvature sensor activity / Retrograde transport at the Trans-Golgi-Network / regulation of respiratory burst / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / GTP-dependent protein binding / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / engulfment of apoptotic cell / NTRK2 activates RAC1 / Inactivation of CDC42 and RAC1 / NADPH oxidase complex / respiratory burst / WNT5:FZD7-mediated leishmania damping / protein localization to phagophore assembly site / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / hepatocyte growth factor receptor signaling pathway / ruffle organization / thioesterase binding / cell projection assembly / regulation of stress fiber assembly / negative regulation of fibroblast migration / RHO GTPases activate CIT / sphingosine-1-phosphate receptor signaling pathway / Nef and signal transduction / motor neuron axon guidance / PCP/CE pathway / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / RHO GTPases activate KTN1 / Activation of RAC1 / regulation of lamellipodium assembly / phosphatidylinositol-4-phosphate binding / Azathioprine ADME / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / positive regulation of Rho protein signal transduction / regulation of cell size / establishment or maintenance of cell polarity / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / NRAGE signals death through JNK / Rac protein signal transduction / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / ficolin-1-rich granule membrane / mitophagy / RHO GTPases Activate NADPH Oxidases / EPH-ephrin mediated repulsion of cells / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / positive regulation of microtubule polymerization / ruffle / EPHB-mediated forward signaling / RAC1 GTPase cycle / regulation of cell migration / actin filament polymerization / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / cell chemotaxis / cell-matrix adhesion / small monomeric GTPase / secretory granule membrane / VEGFR2 mediated vascular permeability / G protein activity / trans-Golgi network membrane / Signal transduction by L1 / actin filament organization / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cell motility / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / intracellular protein transport / neuron migration / MAPK6/MAPK4 signaling / trans-Golgi network / Signaling by SCF-KIT Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tarricone, C. / Xiao, B. / Justin, N. / Gamblin, S.J. / Smerdon, S.J. | ||||||
![]() | ![]() Title: The structural basis of Arfaptin-mediated cross-talk between Rac and Arf signalling pathways. Authors: Tarricone, C. / Xiao, B. / Justin, N. / Walker, P.A. / Rittinger, K. / Gamblin, S.J. / Smerdon, S.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 125.4 KB | Display | ![]() |
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PDB format | ![]() | 96 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 25614.057 Da / Num. of mol.: 2 / Fragment: RESIDUES 118-341 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 21463.143 Da / Num. of mol.: 1 / Mutation: Q61L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-GNP / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.72 % | ||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 Details: Tris, PEG20K, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 24937 / Num. obs: 24501 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 77 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.38 / % possible all: 94.8 |
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Processing
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Refinement | Method to determine structure: molecular replacement / MAD / Resolution: 2.6→20 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): 2 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.3 |