+Open data
-Basic information
Entry | Database: PDB / ID: 2p2l | ||||||
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Title | Rac1-GDP-Zinc Complex | ||||||
Components | Ras-related C3 botulinum toxin substrate 1 | ||||||
Keywords | UNKNOWN FUNCTION / Rho Family GTPase | ||||||
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 / NADPH oxidase complex / 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 / 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 / negative regulation of fibroblast migration / thioesterase binding / regulation of stress fiber assembly / RHO GTPases activate CIT / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / regulation of nitric oxide biosynthetic process / PCP/CE pathway / Azathioprine ADME / motor neuron axon guidance / RHO GTPases activate KTN1 / positive regulation of neutrophil chemotaxis / regulation of lamellipodium assembly / 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 / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / positive regulation of Rho protein signal transduction / establishment or maintenance of cell polarity / regulation of cell size / DSCAM interactions / Activation of RAC1 downstream of NMDARs / Rho GDP-dissociation inhibitor binding / small GTPase-mediated 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 / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate NADPH Oxidases / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / localization / positive regulation of lamellipodium assembly / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / actin filament polymerization / positive regulation of microtubule polymerization / cell-matrix adhesion / cell chemotaxis / substrate adhesion-dependent cell spreading / small monomeric GTPase / G protein activity / positive regulation of endothelial cell migration / secretory granule membrane / VEGFR2 mediated vascular permeability / Signal transduction by L1 / cell motility / actin filament organization / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / neuron migration / MAPK6/MAPK4 signaling / trans-Golgi network / Signaling by SCF-KIT / response to wounding / Regulation of actin dynamics for phagocytic cup formation / cytoplasmic ribonucleoprotein granule / VEGFA-VEGFR2 Pathway / ruffle membrane / recycling endosome membrane / Constitutive Signaling by Aberrant PI3K in Cancer / melanosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / and molecular replacement / SAD / Resolution: 1.9 Å | ||||||
Authors | Prehna, G. / Stebbins, C.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: A Rac1-GDP trimer complex binds zinc with tetrahedral and octahedral coordination, displacing magnesium. Authors: Prehna, G. / Stebbins, C.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p2l.cif.gz | 144.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p2l.ent.gz | 108.5 KB | Display | PDB format |
PDBx/mmJSON format | 2p2l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/2p2l ftp://data.pdbj.org/pub/pdb/validation_reports/p2/2p2l | HTTPS FTP |
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-Related structure data
Related structure data | 1mh1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | Normally a monomer. In this crystal structure zinc induces a trimer. |
-Components
#1: Protein | Mass: 20789.117 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1 / Plasmid: pGEX4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63000 #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 3.55 Å3/Da / Density % sol: 65.34 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100mM MES pH6.0, 15mM ZnSO4, 10% PEGMME 550., VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 90 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X3A / Wavelength: 1.284 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 30, 2007 Details: Double crystal monochromator. Si(111) or Si(220) options. Sagitall focusing. Cylindrically bent ULE mirror with Pt and Rh coating. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double flat crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.284 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 4.1 % / Av σ(I) over netI: 8.6 / Number: 555099 / Rmerge(I) obs: 0.085 / Χ2: 1.01 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 135270 / % possible obs: 99.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.9→77.62 Å / Num. obs: 70803 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 3.7 / % possible all: 100 |
-Phasing
Phasing | Method: SAD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MAD set site |
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Phasing MR |
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Phasing dm | FOM : 0.78 / FOM acentric: 0.8 / FOM centric: 0.67 / Reflection: 30529 / Reflection acentric: 27245 / Reflection centric: 3284 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: and molecular replacement Starting model: 1MH1 Resolution: 1.9→77.62 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.917 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.11 / 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: 27.003 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→77.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 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 |
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