+Open data
-Basic information
Entry | Database: PDB / ID: 6agp | |||||||||
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Title | Structure of Rac1 in the low-affinity state for Mg2+ | |||||||||
Components | Ras-related C3 botulinum toxin substrate 1 | |||||||||
Keywords | SIGNALING PROTEIN / Nucleotide Binding / Gtpase Activity / GTP Binding | |||||||||
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 | SOLUTION NMR / simulated annealing | |||||||||
Authors | Toyama, Y. / Kontani, K. / Katada, T. / Shimada, I. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Sci Adv / Year: 2019 Title: Conformational landscape alternations promote oncogenic activities of Ras-related C3 botulinum toxin substrate 1 as revealed by NMR. Authors: Toyama, Y. / Kontani, K. / Katada, T. / Shimada, I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6agp.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6agp.ent.gz | 968.5 KB | Display | PDB format |
PDBx/mmJSON format | 6agp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/6agp ftp://data.pdbj.org/pub/pdb/validation_reports/ag/6agp | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 20032.338 Da / Num. of mol.: 1 / Mutation: E31C, D63C, Q74C, L160C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1, TC25, MIG5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RP+ / References: UniProt: P63000 |
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#2: Chemical | ChemComp-GDP / |
#3: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Sample state: isotropic / Type: 2D HSQC |
-Sample preparation
Details | Type: solution Contents: 20 mM HEPES, 5 mM MgCl2, 0.5 mM GDP, 0.1 mM DSS, 90% H2O/10% D2O Label: 2H_15N_IALVMmethyl13C_sample / Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0 mM / Label: conditions_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 313 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 3 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |