+Open data
-Basic information
Entry | Database: PDB / ID: 1.0E+96 | ||||||
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Title | Structure of the Rac/p67phox complex | ||||||
Components |
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Keywords | SIGNALING PROTEIN / SIGNALLING COMPLEX / GTPASE / NADPH OXIDASE / PROTEIN-PROTEIN COMPLEX / TPR MOTIF | ||||||
Function / homology | Function and homology information superoxide-generating NADPH oxidase activator activity / superoxide-generating NAD(P)H oxidase activity / phagolysosome / regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / Cross-presentation of particulate exogenous antigens (phagosomes) / NADPH oxidase complex ...superoxide-generating NADPH oxidase activator activity / superoxide-generating NAD(P)H oxidase activity / phagolysosome / regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / Cross-presentation of particulate exogenous antigens (phagosomes) / 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 / ROS and RNS production in phagocytes / cell projection assembly / thioesterase binding / negative regulation of fibroblast migration / regulation of stress fiber assembly / RHO GTPases activate CIT / Nef and signal transduction / superoxide anion generation / sphingosine-1-phosphate receptor signaling pathway / PCP/CE pathway / motor neuron axon guidance / RHO GTPases activate KTN1 / regulation of nitric oxide biosynthetic process / 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 / superoxide metabolic process / Rac protein signal transduction / Detoxification of Reactive Oxygen Species / 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 / RAC3 GTPase cycle / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / localization / cellular defense response / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / phagocytosis / 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 chemotaxis / substrate adhesion-dependent cell spreading / cell-matrix adhesion / small monomeric GTPase / G protein activity / positive regulation of endothelial cell migration / secretory granule membrane / acrosomal vesicle / VEGFR2 mediated vascular permeability / Signal transduction by L1 / cell projection / actin filament organization / cell motility / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of actin cytoskeleton organization Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Lapouge, K. / Smith, S.J.M. / Walker, P.A. / Gamblin, S.J. / Smerdon, S.J. / Rittinger, K. | ||||||
Citation | Journal: Mol.Cell / Year: 2000 Title: Structure of the TPR domain of p67phox in complex with Rac.GTP. Authors: Lapouge, K. / Smith, S.J. / Walker, P.A. / Gamblin, S.J. / Smerdon, S.J. / Rittinger, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e96.cif.gz | 89.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e96.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 1e96.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/1e96 ftp://data.pdbj.org/pub/pdb/validation_reports/e9/1e96 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21429.062 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P15154, UniProt: P63000*PLUS |
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#2: Protein | Mass: 23490.471 Da / Num. of mol.: 1 / Fragment: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-4T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P19878 |
#3: Chemical | ChemComp-GTP / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
Compound details | CHAIN A ENGINEERED MUTATION MET1PRO, GLN61LEU RAC1 ARE GTP-BINDING PROTEINS ASSOCIATED WITH PLASMA ...CHAIN A ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 54.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 10.5 Details: 0.1 M CAPS PH 10.5, 0.2 M LI ACETATE, 0.8 M NAH2PO4, 1.2 M K2HPO4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→15 Å / Num. obs: 123873 / % possible obs: 94 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.4→2.45 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.2 / % possible all: 100 |
Reflection | *PLUS Num. obs: 20975 / Num. measured all: 123873 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MH1, 1A17 Resolution: 2.4→15 Å / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.411 / ESU R Free: 0.288
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Displacement parameters | Biso mean: 29.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→15 Å
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Refine LS restraints |
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