|Entry||Database: PDB / ID: 4gzm|
|Title||Crystal structure of RAC1 F28L mutant|
|Components||Ras-related C3 botulinum toxin substrate 1|
|Keywords||HYDROLASE / Rossmann fold / GTP binding / membrane|
|Function / homology|
Function and homology information
regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / engulfment of apoptotic cell / regulation of hydrogen peroxide metabolic process / ruffle assembly ...regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / engulfment of apoptotic cell / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / Rho GDP-dissociation inhibitor binding / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / respiratory burst / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / PCP/CE pathway / cell projection assembly / RHO GTPases activate CIT / RHO GTPases activate KTN1 / cortical cytoskeleton organization / ruffle organization / hepatocyte growth factor receptor signaling pathway / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / Azathioprine ADME / regulation of stress fiber assembly / negative regulation of fibroblast migration / sphingosine-1-phosphate receptor signaling pathway / thioesterase binding / Wnt signaling pathway, planar cell polarity pathway / regulation of lamellipodium assembly / Nef and signal transduction / motor neuron axon guidance / Sema4D mediated inhibition of cell attachment and migration / Activation of RAC1 / positive regulation of Rho protein signal transduction / positive regulation of cell-substrate adhesion / Ephrin signaling / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / CD28 dependent Vav1 pathway / lamellipodium assembly / Activation of RAC1 downstream of NMDARs / semaphorin-plexin signaling pathway / NRAGE signals death through JNK / regulation of cell size / Rac protein signal transduction / DSCAM interactions / positive regulation of lamellipodium assembly / establishment or maintenance of cell polarity / small GTPase mediated signal transduction / RHO GTPases activate PAKs / ficolin-1-rich granule membrane / positive regulation of focal adhesion assembly / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / RHO GTPases activate IQGAPs / anatomical structure morphogenesis / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / RHO GTPases Activate WASPs and WAVEs / RHO GTPases Activate NADPH Oxidases / RHO GTPases activate PKNs / localization / regulation of actin cytoskeleton organization / GPVI-mediated activation cascade / EPHB-mediated forward signaling / positive regulation of microtubule polymerization / G protein activity / positive regulation of stress fiber assembly / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / RAC1 GTPase cycle / neuron migration / actin filament polymerization / small monomeric GTPase / cell-matrix adhesion / substrate adhesion-dependent cell spreading / cell motility / actin filament organization / secretory granule membrane / RHO GTPases Activate Formins / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of endothelial cell migration / Signal transduction by L1 / cell projection / FCERI mediated MAPK activation / MAPK6/MAPK4 signaling / FCGR3A-mediated phagocytosis / Signaling by SCF-KIT / trans-Golgi network / extrinsic component of cytoplasmic side of plasma membrane / cytoplasmic ribonucleoprotein granule / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / ruffle membrane / actin cytoskeleton organization / response to wounding / recycling endosome membrane
Similarity search - Function
small GTPase Rho family profile. / Small GTPase Rho / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å|
|Authors||Ha, B.H. / Boggon, T.J.|
|Citation||Journal: Proc.Natl.Acad.Sci.USA / Year: 2013|
Title: RAC1P29S is a spontaneously activating cancer-associated GTPase.
Authors: Davis, M.J. / Ha, B.H. / Holman, E.C. / Halaban, R. / Schlessinger, J. / Boggon, T.J.
|Structure viewer||Molecule: |
Downloads & links
A: Ras-related C3 botulinum toxin substrate 1
B: Ras-related C3 botulinum toxin substrate 1
A: Ras-related C3 botulinum toxin substrate 1
B: Ras-related C3 botulinum toxin substrate 1
|Noncrystallographic symmetry (NCS)||NCS domain: |
NCS domain segments:
Mass: 22700.025 Da / Num. of mol.: 2 / Fragment: UNP residues 2-177 / Mutation: F28L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1, TC25, MIG5 / Plasmid: modified pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RILP / References: UniProt: P63000, small monomeric GTPase
Mass: 539.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.27 Å3/Da / Density % sol: 45.78 %|
|Crystal grow||Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 |
Details: 16-18% PEG4000, 8% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97922 Å|
|Detector||Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2012 / Details: mirror|
|Radiation||Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.97922 Å / Relative weight: 1|
|Reflection||Resolution: 2.8→27.823 Å / Num. all: 10053 / Num. obs: 10037 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 99.9 Å2 / Rmerge(I) obs: 0.119 / Rsym value: 0.119 / Net I/σ(I): 7.591|
|Reflection shell||Resolution: 2.8→2.91 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.578 / % possible all: 99.9|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: PDB ENTRY 3TH5
Resolution: 2.8→27.823 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.925 / SU B: 33.989 / SU ML: 0.573 / Cross valid method: THROUGHOUT / ESU R Free: 0.445 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
|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: 106.461 Å2|
|Refinement step||Cycle: LAST / Resolution: 2.8→27.823 Å|
|Refine LS restraints|
|Refine LS restraints NCS|
Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
|LS refinement shell||Resolution: 2.8→2.873 Å / Total num. of bins used: 20 |
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