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Yorodumi- PDB-2wkr: Structure of a photoactivatable Rac1 containing the Lov2 C450M Mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wkr | ||||||
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Title | Structure of a photoactivatable Rac1 containing the Lov2 C450M Mutant | ||||||
Components | NPH1-1, RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 | ||||||
Keywords | TRANSFERASE / CELL ADHESION / NUCLEOTIDE-BINDING / PROTEIN ENGINEERING / RAS SUPERFAMILY LOV2 / PHOTOTROPIN1 / PROTEIN DESIGN / SMALL G-PROTEIN / LIGHT-INDUCED SIGNAL TRANSDUCTION / GTPASE / RHO FAMILY / ATP-BINDING / PRENYLATION / CHIMERA / NUCLEOTIDE-BINDING PROTEIN ENGINEERING / ADP-RIBOSYLATION | ||||||
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 / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / engulfment of apoptotic cell / 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 / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / engulfment of apoptotic cell / NTRK2 activates RAC1 / blue light photoreceptor activity / Inactivation of CDC42 and RAC1 / NADPH oxidase complex / respiratory burst / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / hepatocyte growth factor receptor signaling pathway / ruffle organization / cell projection assembly / thioesterase binding / regulation of stress fiber assembly / negative regulation of fibroblast migration / RHO GTPases activate CIT / sphingosine-1-phosphate receptor signaling pathway / Nef and signal transduction / motor neuron axon guidance / PCP/CE pathway / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / RHO GTPases activate KTN1 / Activation of RAC1 / regulation of lamellipodium assembly / Azathioprine ADME / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / 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 / regulation of cell size / establishment or maintenance of cell polarity / 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 / Sema3A PAK dependent Axon repulsion / ficolin-1-rich granule membrane / RHO GTPases Activate NADPH Oxidases / EPH-ephrin mediated repulsion of cells / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / 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 / Signal transduction by L1 / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / positive regulation of microtubule polymerization / EPHB-mediated forward signaling / RAC1 GTPase cycle / regulation of cell migration / actin filament polymerization / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / cell chemotaxis / cell-matrix adhesion / small monomeric GTPase / secretory granule membrane / VEGFR2 mediated vascular permeability / G protein activity / actin filament organization / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cell motility / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / ruffle membrane / neuron migration / MAPK6/MAPK4 signaling / trans-Golgi network / Signaling by SCF-KIT / Regulation of actin dynamics for phagocytic cup formation / Constitutive Signaling by Aberrant PI3K in Cancer / VEGFA-VEGFR2 Pathway / response to wounding / cytoplasmic ribonucleoprotein granule / recycling endosome membrane / PIP3 activates AKT signaling / Factors involved in megakaryocyte development and platelet production Similarity search - Function | ||||||
Biological species | AVENA SATIVA (oats) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Wu, Y.I. / Frey, D. / Lungu, O.I. / Jaehrig, A. / Schlichting, I. / Kuhlman, B. / Hahn, K.M. | ||||||
Citation | Journal: Nature / Year: 2009 Title: A Genetically Encoded Photoactivatable Rac Controls the Motility of Living Cells. Authors: Wu, Y.I. / Frey, D. / Lungu, O.I. / Jaehrig, A. / Schlichting, I. / Kuhlman, B. / Hahn, K.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wkr.cif.gz | 87.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wkr.ent.gz | 63.1 KB | Display | PDB format |
PDBx/mmJSON format | 2wkr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wkr_validation.pdf.gz | 984.6 KB | Display | wwPDB validaton report |
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Full document | 2wkr_full_validation.pdf.gz | 988.2 KB | Display | |
Data in XML | 2wkr_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 2wkr_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/2wkr ftp://data.pdbj.org/pub/pdb/validation_reports/wk/2wkr | HTTPS FTP |
-Related structure data
Related structure data | 2wkpC 2wkqC 1mh1S 2vouS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37631.035 Da / Num. of mol.: 1 Fragment: NPH1-1, RESIDUES 404-546 AND P21-RAC1, RESIDUES 4-180 Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) AVENA SATIVA (oats), (gene. exp.) HOMO SAPIENS (human) Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL10 GOLD / References: UniProt: O49003, UniProt: P63000 |
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-Non-polymers , 5 types, 220 molecules
#2: Chemical | ChemComp-GTP / | ||
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#3: Chemical | ChemComp-FMN / | ||
#4: Chemical | ChemComp-MG / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 450 TO MET ENGINEERED RESIDUE IN CHAIN A, GLN 61 TO LEU ...ENGINEERED |
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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: 3.46 Å3/Da / Density % sol: 64.5 % / Description: NONE |
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Crystal grow | Details: 18 % (V/V) PEG 600 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9797 |
Detector | Type: MARRESEARCH MX-225 / Detector: CCD / Date: Oct 11, 2008 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 25771 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1MH1, 2VOU Resolution: 2.2→32.601 Å / SU ML: 0.26 / σ(F): 1.99 / Phase error: 20.62 / 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 / Bsol: 38.656 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→32.601 Å
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Refine LS restraints |
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LS refinement shell |
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