+Open data
-Basic information
Entry | Database: PDB / ID: 2w2v | ||||||
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Title | Rac2 (G12V) in complex with GTPgS | ||||||
Components | RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 2 | ||||||
Keywords | SIGNALING PROTEIN / ADP-RIBOSYLATION / CYTOPLASM / DISEASE MUTATION / GTP-BINDING / LIPOPROTEIN / METHYLATION / NUCLEOTIDE-BINDING / POLYMORPHISM / PRENYLATION / PHOSPHOLIPASE C / PHOSPHOINOSITIDES / RHO | ||||||
Function / homology | Function and homology information regulation of mast cell chemotaxis / regulation of cell-substrate adhesion / lymphocyte aggregation / erythrocyte enucleation / positive regulation of mast cell proliferation / regulation of respiratory burst / regulation of neutrophil migration / mast cell proliferation / regulation of mast cell degranulation / NADPH oxidase complex ...regulation of mast cell chemotaxis / regulation of cell-substrate adhesion / lymphocyte aggregation / erythrocyte enucleation / positive regulation of mast cell proliferation / regulation of respiratory burst / regulation of neutrophil migration / mast cell proliferation / regulation of mast cell degranulation / NADPH oxidase complex / regulation of hydrogen peroxide metabolic process / respiratory burst / protein kinase regulator activity / ROS and RNS production in phagocytes / cell projection assembly / PCP/CE pathway / positive regulation of neutrophil chemotaxis / positive regulation of protein targeting to mitochondrion / small GTPase-mediated signal transduction / regulation of T cell proliferation / RHO GTPases Activate NADPH Oxidases / RAC2 GTPase cycle / positive regulation of lamellipodium assembly / regulation of cell migration / bone resorption / GPVI-mediated activation cascade / actin filament organization / phagocytic vesicle membrane / Constitutive Signaling by Aberrant PI3K in Cancer / chemotaxis / PIP3 activates AKT signaling / lamellipodium / nuclear envelope / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / mitochondrial outer membrane / G protein-coupled receptor signaling pathway / focal adhesion / GTPase activity / GTP binding / endoplasmic reticulum membrane / signal transduction / extracellular exosome / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Opaleye, O. / Bunney, T.D. / Roe, S.M. / Pearl, L.H. | ||||||
Citation | Journal: Mol.Cell / Year: 2009 Title: Structural Insights Into Formation of an Active Signaling Complex between Rac and Phospholipase C Gamma 2. Authors: Bunney, T.D. / Opaleye, O. / Roe, S.M. / Vatter, P. / Baxendale, R.W. / Walliser, C. / Everett, K.L. / Josephs, M.B. / Christow, C. / Rodrigues-Lima, F. / Gierschik, P. / Pearl, L.H. / Katan, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w2v.cif.gz | 150.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w2v.ent.gz | 124.2 KB | Display | PDB format |
PDBx/mmJSON format | 2w2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/2w2v ftp://data.pdbj.org/pub/pdb/validation_reports/w2/2w2v | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 20241.234 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-177 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P15153 #2: Chemical | ChemComp-GTP / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, GLY 12 TO VAL ENGINEERED RESIDUE IN CHAIN B, GLY 12 TO VAL ...ENGINEERED | Sequence details | THERE IS TAG LINKER SEQUENCE, GGGSGGS (NOT SEEN) AND A MUTATION G12V | |
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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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | Temperature: 293 K / pH: 7 Details: RAC2(2-177)GTPGS WAS CRYSTALLIZED USING A PROTEIN CONCENTRATION OF 25 MG/ML WITH PRECIPITANT (18% PEG3350, 300 MM SODIUM/POTASSIUM TARTRATE) AND AT A CONSTANT TEMPERATURE OF 20C |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 13, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→54 Å / Num. obs: 79004 / % possible obs: 98.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 20.98 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.3 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN HOUSE RAC2 STRUCTURE Resolution: 2→53.62 Å / SU ML: 0.45 / σ(F): 1.12 / Phase error: 40.6 / Stereochemistry target values: ML Details: DATA INITIALLY THOUGHT TO BE P212121, LATER FOUND TO BE P21 WITH B AS 90, ALSO TWINNED.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.57 Å2 / ksol: 0.35 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→53.62 Å
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Refine LS restraints |
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LS refinement shell |
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