+Open data
-Basic information
Entry | Database: PDB / ID: 5n6o | ||||||
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Title | Wild type human Rac1-GDP | ||||||
Components | Ras-related C3 botulinum toxin substrate 1 | ||||||
Keywords | PROTEIN BINDING / Rac / GTPase / GDP / guanine exchange factor / GEF | ||||||
Function / homology | Function and homology information regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 ...regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / engulfment of apoptotic cell / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / respiratory burst / hepatocyte growth factor receptor signaling pathway / ruffle organization / cell projection assembly / thioesterase binding / negative regulation of fibroblast migration / regulation of stress fiber assembly / RHO GTPases activate CIT / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / regulation of nitric oxide biosynthetic process / PCP/CE pathway / motor neuron axon guidance / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / positive regulation of neutrophil chemotaxis / Azathioprine ADME / Activation of RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / MET activates RAP1 and RAC1 / 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 / establishment or maintenance of cell polarity / regulation of cell size / DSCAM interactions / 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 / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate NADPH Oxidases / RHO GTPases Activate WASPs and WAVEs / anatomical structure morphogenesis / RHO GTPases activate IQGAPs / localization / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / actin filament polymerization / cell-matrix adhesion / cell chemotaxis / substrate adhesion-dependent cell spreading / small monomeric GTPase / G protein activity / positive regulation of endothelial cell migration / secretory granule membrane / VEGFR2 mediated vascular permeability / Signal transduction by L1 / actin filament organization / cell motility / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / neuron migration / MAPK6/MAPK4 signaling / trans-Golgi network / Signaling by SCF-KIT / cytoplasmic ribonucleoprotein granule / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / VEGFA-VEGFR2 Pathway / response to wounding / recycling endosome membrane / Constitutive Signaling by Aberrant PI3K in Cancer / melanosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Cherfils, J. / Ferrandez, Y. | ||||||
Funding support | France, 1items
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Citation | Journal: Sci Rep / Year: 2017 Title: Allosteric inhibition of the guanine nucleotide exchange factor DOCK5 by a small molecule. Authors: Ferrandez, Y. / Zhang, W. / Peurois, F. / Akendengue, L. / Blangy, A. / Zeghouf, 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 | 5n6o.cif.gz | 81.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n6o.ent.gz | 64.4 KB | Display | PDB format |
PDBx/mmJSON format | 5n6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/5n6o ftp://data.pdbj.org/pub/pdb/validation_reports/n6/5n6o | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19579.568 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1, TC25, MIG5 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P63000 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.14 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0,1 mM MES ph 6.5 PEG 3350 20% |
-Data collection
Diffraction | Mean temperature: 291.15 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.586→65.158 Å / Num. obs: 11873 / % possible obs: 99.5 % / Redundancy: 6 % / Net I/σ(I): 8.4 |
Reflection scale | Group code: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→44.59 Å / Cor.coef. Fo:Fc: 0.862 / Cor.coef. Fo:Fc free: 0.821 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.392 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.592 / SU Rfree Blow DPI: 0.319 / SU Rfree Cruickshank DPI: 0.319
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Displacement parameters | Biso max: 120.3 Å2 / Biso mean: 40.4 Å2 / Biso min: 8.25 Å2
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Refine analyze | Luzzati coordinate error obs: 0 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.59→44.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.59→2.84 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
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