|Entry||Database: PDB / ID: 1g4u|
|Title||CRYSTAL STRUCTURE OF THE SALMONELLA TYROSINE PHOSPHATASE AND GTPASE ACTIVATING PROTEIN SPTP BOUND TO RAC1|
|Keywords||SIGNALING PROTEIN / virulence factor / GAP / tyrosine phosphatase / 4-helix bundle / GTPase|
|Function / homology|
Function and homology information
regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / regulation of hydrogen peroxide metabolic process / Activated NTRK2 signals through CDK5 / localization within membrane / negative regulation of fibroblast migration / negative regulation of receptor-mediated endocytosis / mast cell chemotaxis / Rac protein signal transduction ...regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / regulation of hydrogen peroxide metabolic process / Activated NTRK2 signals through CDK5 / localization within membrane / negative regulation of fibroblast migration / negative regulation of receptor-mediated endocytosis / mast cell chemotaxis / Rac protein signal transduction / ruffle assembly / engulfment of apoptotic cell / Rho GDP-dissociation inhibitor binding / NTRK2 activates RAC1 / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / PCP/CE pathway / RHO GTPases activate CIT / RHO GTPases activate KTN1 / ruffle organization / positive regulation of neutrophil chemotaxis / cortical cytoskeleton organization / hepatocyte growth factor receptor signaling pathway / thioesterase binding / regulation of nitric oxide biosynthetic process / regulation of stress fiber assembly / sphingosine-1-phosphate receptor signaling pathway / Wnt signaling pathway, planar cell polarity pathway / motor neuron axon guidance / cell projection assembly / Nef and signal transduction / Sema4D mediated inhibition of cell attachment and migration / regulation of lamellipodium assembly / positive regulation of Rho protein signal transduction / positive regulation of cell-substrate adhesion / Activation of RAC1 / Ephrin signaling / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / lamellipodium assembly / semaphorin-plexin signaling pathway / Activation of RAC1 downstream of NMDARs / CD28 dependent Vav1 pathway / regulation of cell size / NRAGE signals death through JNK / establishment or maintenance of cell polarity / DSCAM interactions / positive regulation of lamellipodium assembly / small GTPase mediated signal transduction / ficolin-1-rich granule membrane / RHO GTPases activate PAKs / positive regulation of insulin secretion involved in cellular response to glucose stimulus / bone resorption / RHO GTPases activate IQGAPs / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of focal adhesion assembly / positive regulation of microtubule polymerization / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / RHO GTPases Activate NADPH Oxidases / cell motility / regulation of actin cytoskeleton organization / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / neuron migration / actin filament polymerization / G protein activity / small monomeric GTPase / GPVI-mediated activation cascade / EPHB-mediated forward signaling / positive regulation of DNA replication / regulation of cell migration / RAC1 GTPase cycle / cell-matrix adhesion / GTPase activator activity / substrate adhesion-dependent cell spreading / cell projection / protein-tyrosine-phosphatase / VEGFR2 mediated vascular permeability / secretory granule membrane / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament organization / protein tyrosine phosphatase activity / Signal transduction by L1 / positive regulation of endothelial cell migration / cytoplasmic ribonucleoprotein granule / FCERI mediated MAPK activation / MAPK6/MAPK4 signaling / FCGR3A-mediated phagocytosis / trans-Golgi network / Signaling by SCF-KIT / ruffle membrane / actin cytoskeleton organization / response to wounding / extrinsic component of cytoplasmic side of plasma membrane
Similarity search - Function
SicP binding / Secreted effector protein SptP, N-terminal domain / Virulence factor YopE uncharacterised domain / Virulence factor YopE, GAP domain superfamily / Virulence factor YopE, GAP domain / Yersinia virulence determinant (YopE) / Type III secreted modular tyrosine phosphatase, SptP/YopH / Globular protein, non-globular alpha/beta subunit / small GTPase Rho family profile. / Small GTPase Rho ...SicP binding / Secreted effector protein SptP, N-terminal domain / Virulence factor YopE uncharacterised domain / Virulence factor YopE, GAP domain superfamily / Virulence factor YopE, GAP domain / Yersinia virulence determinant (YopE) / Type III secreted modular tyrosine phosphatase, SptP/YopH / Globular protein, non-globular alpha/beta subunit / small GTPase Rho family profile. / Small GTPase Rho / Protein tyrosine phosphatase superfamily / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain motif / Protein-tyrosine phosphatase, catalytic / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Four Helix Bundle (Hemerythrin (Met), subunit A) / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Complex / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ras-related C3 botulinum toxin substrate 1 / ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / Secreted effector protein SptP
Similarity search - Component
|Biological species||Salmonella typhimurium (bacteria)|
Homo sapiens (human)
|Method||X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å|
|Authors||Stebbins, C.E. / Galan, J.E.|
|Citation||Journal: Mol.Cell / Year: 2000|
Title: Modulation of host signaling by a bacterial mimic: structure of the Salmonella effector SptP bound to Rac1.
Authors: Stebbins, C.E. / Galan, J.E.
|Structure viewer||Molecule: |
Downloads & links
S: PROTEIN TYROSINE PHOSPHATASE SPTP
R: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
-Protein , 2 types, 2 molecules S
|#1: Protein|| |
Mass: 42127.801 Da / Num. of mol.: 1 / Fragment: SPTP RESIDUES 161-543
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: SPTP / Plasmid: PGEX-4T-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P74873
|#2: Protein|| |
Mass: 20402.650 Da / Num. of mol.: 1 / Fragment: RAC1 RESIDUES 1-184 / Mutation: F78S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1 / Plasmid: PGEX-4T-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P63000
-Non-polymers , 4 types, 337 molecules
|#3: Chemical|| ChemComp-MG / |
|#4: Chemical|| ChemComp-GDP / |
|#5: Chemical|| ChemComp-AF3 / |
|#6: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.63 Å3/Da / Density % sol: 53.31 %|
|Crystal grow||Method: vapor diffusion, hanging drop / pH: 5.7 |
Details: 18 %PEG 400, 0.1M MES, 15mM sodium flouride, 0.1mM aluminum chloride, 2mM DTT, 2mM magnesium chloride, pH 5.7, VAPOR DIFFUSION, HANGING DROP
*PLUSDensity % sol: 50 %
|Components of the solutions|
|Diffraction||Mean temperature: 113 K|
|Diffraction source||Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å|
|Detector||Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 17, 2000 / Details: Yale mirrors|
|Radiation||Monochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 1.5418 Å / Relative weight: 1|
|Reflection||Resolution: 2.3→50 Å / Num. all: 28370 / Num. obs: 27264 / % possible obs: 96.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 15.13 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 13|
|Reflection shell||Resolution: 2.3→2.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 3.7 / % possible all: 94|
*PLUSNum. measured all: 177445
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber|
|Refinement step||Cycle: LAST / Resolution: 2.3→50 Å|
|Refine LS restraints|
|LS refinement shell||Resolution: 2.3→2.33 Å / |
*PLUSName: CNS / Classification: refinement
*PLUSHighest resolution: 2.3 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 7.5 %
|Refine LS restraints|
*PLUSType: c_angle_deg / Dev ideal: 1.4
|LS refinement shell|
*PLUSLowest resolution: 2.3 Å / Rfactor Rfree: 0.36 / Rfactor Rwork: 0.285
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