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- PDB-2wkr: Structure of a photoactivatable Rac1 containing the Lov2 C450M Mutant -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wkr | ||||||
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Title | Structure of a photoactivatable Rac1 containing the Lov2 C450M Mutant | ||||||
![]() | NPH1-1, RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 | ||||||
![]() | 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 | ![]() regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / blue light photoreceptor activity / 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 / blue light photoreceptor activity / 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 / 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 / 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 / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / RHO GTPases activate KTN1 / Activation of RAC1 / motor neuron axon guidance / 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 / 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 / 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 / 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 / regulation of cell migration / positive regulation of microtubule polymerization / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / RAC1 GTPase cycle / actin filament polymerization / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / cell-matrix adhesion / cell chemotaxis / small monomeric GTPase / secretory granule membrane / VEGFR2 mediated vascular permeability / G protein activity / 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 / trans-Golgi network / Signaling by SCF-KIT / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule / response to wounding / recycling endosome membrane / Constitutive Signaling by Aberrant PI3K in Cancer Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, Y.I. / Frey, D. / Lungu, O.I. / Jaehrig, A. / Schlichting, I. / Kuhlman, B. / Hahn, K.M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.4 KB | Display | ![]() |
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PDB format | ![]() | 63.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 984.6 KB | Display | ![]() |
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Full document | ![]() | 988.2 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 22.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wkpC ![]() 2wkqC ![]() 1mh1S ![]() 2vouS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() Plasmid: PQE30 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 220 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
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#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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