+Open data
-Basic information
Entry | Database: PDB / ID: 5a0f | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Yersinia Afp18-modified RhoA | |||||||||
Components | TRANSFORMING PROTEIN RHOA | |||||||||
Keywords | SIGNALING PROTEIN / N-ACETYLGLUCOSAMINE-PROTEIN / TYROSINE GLYCOSYLATION / GTPASE / BACTERIAL TOXIN EFFECTOR / TYPE 6 SECRETION SYSTEM / ANTIFEEDING PROPHAGE | |||||||||
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 / cellular response to chemokine / negative regulation of cell migration involved in sprouting angiogenesis / beta selection / regulation of modification of postsynaptic structure / establishment of epithelial cell apical/basal polarity / negative regulation of cell size / RHO GTPases Activate ROCKs / negative regulation of motor neuron apoptotic process / negative regulation of oxidative phosphorylation / RHO GTPases activate CIT / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / positive regulation of podosome assembly / negative regulation of cell-substrate adhesion / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / positive regulation of alpha-beta T cell differentiation / ossification involved in bone maturation / motor neuron apoptotic process / odontogenesis / wound healing, spreading of cells / PI3K/AKT activation / positive regulation of leukocyte adhesion to vascular endothelial cell / apical junction complex / regulation of focal adhesion assembly / negative chemotaxis / myosin binding / EPHA-mediated growth cone collapse / stress fiber assembly / regulation of neuron projection development / RHOC GTPase cycle / androgen receptor signaling pathway / positive regulation of cytokinesis / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / mitotic spindle assembly / semaphorin-plexin signaling pathway / Rho protein signal transduction / ficolin-1-rich granule membrane / RHOA GTPase cycle / endothelial cell migration / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / cytoplasmic microtubule organization / regulation of microtubule cytoskeleton organization / skeletal muscle tissue development / negative regulation of reactive oxygen species biosynthetic process / regulation of cell migration / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / cell-matrix adhesion / substrate adhesion-dependent cell spreading / kidney development / small monomeric GTPase / G protein activity / secretory granule membrane / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / 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 / VEGFA-VEGFR2 Pathway / positive regulation of non-canonical NF-kappaB signal transduction / G beta:gamma signalling through PI3Kgamma / ruffle membrane / G alpha (12/13) signalling events Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Jank, T. / Schimpl, M. / van Aalten, D.M. | |||||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Tyrosine glycosylation of Rho by Yersinia toxin impairs blastomere cell behaviour in zebrafish embryos. Authors: Jank, T. / Eckerle, S. / Steinemann, M. / Trillhaase, C. / Schimpl, M. / Wiese, S. / van Aalten, D.M. / Driever, W. / Aktories, K. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5a0f.cif.gz | 51.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5a0f.ent.gz | 36 KB | Display | PDB format |
PDBx/mmJSON format | 5a0f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/5a0f ftp://data.pdbj.org/pub/pdb/validation_reports/a0/5a0f | HTTPS FTP |
---|
-Related structure data
Related structure data | 1dpfS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20467.457 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-181 Source method: isolated from a genetically manipulated source Details: GLYCOSYLATION AT Y 34 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX4T / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61586 |
---|---|
#2: Chemical | ChemComp-GDP / |
#3: Chemical | ChemComp-SO4 / |
#4: Sugar | ChemComp-NDG / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | N-ACETYL-D-GLUCOSAMINE (NAG): N-ACETYL-D-GLUCOSAMINE IS COVALENTLY ATTACHED TO THE HYDROXYL GROUP ...N-ACETYL-D-GLUCOSAMIN |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.07 % / Description: NONE |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M SODIUM ACETATE, PH 5 AND 1.5 M AMMONIUM SULFATE; SITTING-DROP VAPOR-DIFFUSION AT 293.15 K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Feb 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 31941 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.5 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DPF Resolution: 2→91.39 Å / SU B: 2.912 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 19.808 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→91.39 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|