+Open data
-Basic information
Entry | Database: PDB / ID: 3lxr | ||||||
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Title | Shigella IpgB2 in complex with human RhoA and GDP (complex C) | ||||||
Components |
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Keywords | Signaling Protein/RHOA-BINDING PROTEIN / IpgB2 / RhoA / GTPase / GEF / GEF-GTPase-complex / WxxxE / TTSS effector protein / bacterial GEF / cytoskeleton dynamics / Signaling Protein-RHOA-BINDING PROTEIN complex | ||||||
Function / homology | Function and homology information aortic valve formation / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / bone trabecula morphogenesis / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / SLIT2:ROBO1 increases RHOA activity ...aortic valve formation / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / bone trabecula morphogenesis / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / regulation of neural precursor cell proliferation / cleavage furrow formation / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / cell junction assembly / apical junction assembly / regulation of systemic arterial blood pressure by endothelin / negative regulation of cell migration involved in sprouting angiogenesis / cellular response to chemokine / negative regulation of cell size / beta selection / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / PCP/CE pathway / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / positive regulation of podosome assembly / negative regulation of cell-substrate adhesion / positive regulation of alpha-beta T cell differentiation / ossification involved in bone maturation / odontogenesis / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / motor neuron apoptotic process / positive regulation of leukocyte adhesion to vascular endothelial cell / PI3K/AKT activation / wound healing, spreading of cells / apical junction complex / regulation of neuron projection development / regulation of focal adhesion assembly / negative chemotaxis / myosin binding / EPHA-mediated growth cone collapse / stress fiber assembly / RHOC GTPase cycle / positive regulation of cytokinesis / cerebral cortex cell migration / androgen receptor signaling pathway / cellular response to cytokine stimulus / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / Rho protein signal transduction / ficolin-1-rich granule membrane / mitotic spindle assembly / RHOA GTPase cycle / endothelial cell migration / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / regulation of microtubule cytoskeleton organization / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / skeletal muscle tissue development / RHO GTPases activate PKNs / regulation of cell migration / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / substrate adhesion-dependent cell spreading / cell-matrix adhesion / small monomeric GTPase / secretory granule membrane / G protein activity / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / cell periphery / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / neuron migration / positive regulation of protein serine/threonine kinase activity / cell morphogenesis / cytoplasmic side of plasma membrane / ruffle membrane / VEGFA-VEGFR2 Pathway / positive regulation of non-canonical NF-kappaB signal transduction / G beta:gamma signalling through PI3Kgamma / G alpha (12/13) signalling events Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Shigella flexneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 Å | ||||||
Authors | Klink, B.U. / Barden, S. / Heidler, T.V. / Borchers, C. / Ladwein, M. / Stradal, T.E.B. / Rottner, K. / Heinz, D.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structure of Shigella IPGB2 in complex with human RhoA: Implications for the mechanism of bacterial GEF-mimicry Authors: Klink, B.U. / Barden, S. / Heidler, T.V. / Borchers, C. / Ladwein, M. / Stradal, T.E.B. / Rottner, K. / Heinz, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lxr.cif.gz | 102.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lxr.ent.gz | 75.5 KB | Display | PDB format |
PDBx/mmJSON format | 3lxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lxr_validation.pdf.gz | 795.8 KB | Display | wwPDB validaton report |
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Full document | 3lxr_full_validation.pdf.gz | 798 KB | Display | |
Data in XML | 3lxr_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 3lxr_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/3lxr ftp://data.pdbj.org/pub/pdb/validation_reports/lx/3lxr | HTTPS FTP |
-Related structure data
Related structure data | 3lw8C 3lwnSC 3lyqC C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 20747.715 Da / Num. of mol.: 1 / Fragment: residues 2-181 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA / Plasmid: pET-28c / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner (DE3) / References: UniProt: P61586 | ||
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#2: Protein | Mass: 21935.990 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipgB2 / Plasmid: pET-M 41 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner (DE3) / References: UniProt: Q9AJW7 | ||
#3: Chemical | ChemComp-GDP / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.18 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% (w/v) PEG 3350; post-crystallization treatment: EDTA, LiSO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 25, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→42.53 Å / Num. obs: 45588 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 23.76 |
Reflection shell | Resolution: 1.68→1.72 Å / Redundancy: 4 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 2.6 / Num. measured obs: 12890 / Num. unique all: 3248 / Num. unique obs: 3248 / % possible all: 96.9 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3LWN Resolution: 1.68→42.53 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.218 / WRfactor Rwork: 0.167 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.859 / SU B: 4.495 / SU ML: 0.07 / SU R Cruickshank DPI: 0.101 / SU Rfree: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): -3 / ESU R: 0.101 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.02 Å2 / Biso mean: 17.277 Å2 / Biso min: 4.28 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→42.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.68→1.724 Å / Total num. of bins used: 20
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Refinement TLS params. | T11: 0.0712 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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