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Yorodumi- PDB-8i5w: Crystal structure of the DHR-2 domain of DOCK10 in complex with Rac1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i5w | ||||||
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Title | Crystal structure of the DHR-2 domain of DOCK10 in complex with Rac1 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / DOCK / GEF / DHR-2 / GTPase / RHO / RAC / CDC42 | ||||||
Function / homology | Function and homology information RAC3 GTPase cycle / RAC2 GTPase cycle / CDC42 GTPase cycle / marginal zone B cell differentiation / RAC1 GTPase cycle / regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 ...RAC3 GTPase cycle / RAC2 GTPase cycle / CDC42 GTPase cycle / marginal zone B cell differentiation / RAC1 GTPase cycle / regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / Inactivation of CDC42 and RAC1 / NADPH oxidase complex / engulfment of apoptotic cell / Factors involved in megakaryocyte development and platelet production / WNT5:FZD7-mediated leishmania damping / respiratory burst / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / hepatocyte growth factor receptor signaling pathway / ruffle organization / dendritic spine morphogenesis / thioesterase binding / regulation of stress fiber assembly / negative regulation of fibroblast migration / cell projection assembly / RHO GTPases activate CIT / sphingosine-1-phosphate receptor signaling pathway / Nef and signal transduction / PCP/CE pathway / regulation of nitric oxide biosynthetic process / positive regulation of neutrophil chemotaxis / RHO GTPases activate KTN1 / Activation of RAC1 / motor neuron axon guidance / regulation of lamellipodium assembly / Azathioprine ADME / MET activates RAP1 and RAC1 / positive regulation of cell-substrate adhesion / DCC mediated attractive signaling / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / regulation of cell size / establishment or maintenance of cell polarity / DSCAM interactions / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / positive regulation of Rho protein signal transduction / NRAGE signals death through JNK / Rac protein signal transduction / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / B cell homeostasis / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / ficolin-1-rich granule membrane / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate NADPH Oxidases / RHO GTPases Activate WASPs and WAVEs / localization / RHO GTPases activate IQGAPs / anatomical structure morphogenesis / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / RHO GTPases activate PKNs / positive regulation of microtubule polymerization / regulation of cell migration / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / actin filament polymerization / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / guanyl-nucleotide exchange factor activity / cell-matrix adhesion / cell chemotaxis / small monomeric GTPase / secretory granule membrane / positive regulation of GTPase activity / G protein activity / VEGFR2 mediated vascular permeability / Signal transduction by L1 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / cell motility / regulation of actin cytoskeleton organization / actin filament organization / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / neuron migration / MAPK6/MAPK4 signaling Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.432 Å | ||||||
Authors | Kukimoto-Niino, M. / Mishima-Tsumagari, C. / Ihara, K. / Fukui, Y. / Yokoyama, S. / Shirouzu, M. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2023 Title: Structural basis for the dual GTPase specificity of the DOCK10 guanine nucleotide exchange factor. Authors: Kukimoto-Niino, M. / Ihara, K. / Mishima-Tsumagari, C. / Inoue, M. / Fukui, Y. / Yokoyama, S. / Shirouzu, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i5w.cif.gz | 196.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i5w.ent.gz | 155.2 KB | Display | PDB format |
PDBx/mmJSON format | 8i5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i5w_validation.pdf.gz | 452.4 KB | Display | wwPDB validaton report |
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Full document | 8i5w_full_validation.pdf.gz | 459.4 KB | Display | |
Data in XML | 8i5w_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | 8i5w_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/8i5w ftp://data.pdbj.org/pub/pdb/validation_reports/i5/8i5w | HTTPS FTP |
-Related structure data
Related structure data | 8i5fSC 8i5vC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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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-Components
#1: Protein | Mass: 32603.924 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dock10, Kiaa0694, Ziz3 / Cell (production host): Cell-free protein synthesis / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BZN6 |
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#2: Protein | Mass: 20230.232 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1, TC25, MIG5 / Cell (production host): Cell-free protein synthesis / Production host: Escherichia coli (E. coli) / References: UniProt: P63000, small monomeric GTPase |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: ammonium sulfate, sodium cacodylate, PEG 8000, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→46.8 Å / Num. obs: 23123 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rrim(I) all: 0.331 / Net I/σ(I): 8.69 |
Reflection shell | Resolution: 2.43→2.58 Å / Rmerge(I) obs: 0.996 / Num. unique obs: 3630 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8i5f Resolution: 2.432→46.778 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0.6 / Phase error: 31.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.432→46.778 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 6.351 Å / Origin y: 28.8533 Å / Origin z: -22.826 Å
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Refinement TLS group | Selection details: all |