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Yorodumi- PDB-2nz8: N-terminal DHPH cassette of Trio in complex with nucleotide-free Rac1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nz8 | ||||||
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Title | N-terminal DHPH cassette of Trio in complex with nucleotide-free Rac1 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / CELL CYCLE / Trio / Rac1 / Dbl-family GEF / Rho-family GTPase / DH/PH cassette | ||||||
Function / homology | Function and homology information cell surface receptor protein tyrosine phosphatase signaling pathway / 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 ...cell surface receptor protein tyrosine phosphatase signaling pathway / 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 / 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 / regulation of small GTPase mediated signal transduction / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / positive regulation of Rho protein signal transduction / negative regulation of fat cell differentiation / establishment or maintenance of cell polarity / regulation of cell size / DSCAM interactions / extrinsic component of membrane / Activation of RAC1 downstream of NMDARs / Rho GDP-dissociation inhibitor binding / small GTPase-mediated signal transduction / postsynaptic modulation of chemical synaptic transmission / presynaptic active zone / NRAGE signals death through JNK / Rac protein signal transduction / RHOJ GTPase cycle / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / CDC42 GTPase cycle / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate NADPH Oxidases / RHOA GTPase cycle / RHO GTPases Activate WASPs and WAVEs / anatomical structure morphogenesis / RAC3 GTPase cycle / RAC2 GTPase cycle / 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 chemotaxis / substrate adhesion-dependent cell spreading / guanyl-nucleotide exchange factor activity / cell-matrix adhesion / small monomeric GTPase / neuron projection morphogenesis / G protein activity / positive regulation of endothelial cell migration / secretory granule membrane / 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Chhatriwala, M.K. / Betts, L. / Worthylake, D.K. / Sondek, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: The DH and PH Domains of Trio Coordinately Engage Rho GTPases for their Efficient Activation Authors: Chhatriwala, M.K. / Betts, L. / Worthylake, D.K. / Sondek, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nz8.cif.gz | 210.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nz8.ent.gz | 168.5 KB | Display | PDB format |
PDBx/mmJSON format | 2nz8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/2nz8 ftp://data.pdbj.org/pub/pdb/validation_reports/nz/2nz8 | 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 on special symmetry positions |
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Details | There is one biological unit in each assymetric unit (complex between Rac1 and Trio DH/PH) |
-Components
#1: Protein | Mass: 19710.764 Da / Num. of mol.: 1 / Fragment: soluble part (residues 1-177) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P63000 |
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#2: Protein | Mass: 36561.953 Da / Num. of mol.: 1 / Fragment: N-terminal DH/PH cassette (residues 1226-1535) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRIO / Plasmid: pPROEX-HTa / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O75962 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.01 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6 Details: 100 mM sodium cacodylate pH 5.5 to 6.5, 14 to 18% (w/v) PEG 8000, and 300-500 mM calcium acetate, pH 6.0, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0712 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 29, 2004 |
Radiation | Monochromator: double crystal Si (220) cryogenically cooled monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0712 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 39574 / Num. obs: 39416 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rsym value: 0.069 / Χ2: 1.824 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.53 / Num. unique all: 3903 / Rsym value: 0.524 / Χ2: 1.124 / % possible all: 99.8 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: residues 1231-1390 of PDB entry 1NTY and residues 1-177 of PDB entry 1FOE Resolution: 2→19.41 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.565 / SU ML: 0.111 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 41.241 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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