[English] 日本語
Yorodumi- PDB-4xh9: CRYSTAL STRUCTURE OF HUMAN RHOA IN COMPLEX WITH DH/PH FRAGMENT OF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xh9 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF HUMAN RHOA IN COMPLEX WITH DH/PH FRAGMENT OF THE GUANINE NUCLEOTIDE EXCHANGE FACTOR NET1 | ||||||
Components |
| ||||||
Keywords | SIGNALING PROTEIN / RHOA GTPASE / ACTIVATOR / GUANINE NUCLEOTIDE EXCHANGE FACTOR | ||||||
Function / homology | Function and homology information myoblast migration / 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 ...myoblast migration / 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 / 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 / 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 / regulation of small GTPase mediated signal transduction / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / ossification involved in bone maturation / positive regulation of alpha-beta T cell differentiation / odontogenesis / motor neuron apoptotic process / positive regulation of leukocyte adhesion to vascular endothelial cell / PI3K/AKT activation / wound healing, spreading of cells / regulation of neuron projection development / regulation of focal adhesion assembly / apical junction complex / negative chemotaxis / positive regulation of Rho protein signal transduction / RHOB GTPase cycle / myosin binding / NRAGE signals death through JNK / EPHA-mediated growth cone collapse / stress fiber assembly / RHOC GTPase cycle / positive regulation of cytokinesis / androgen receptor signaling pathway / cerebral cortex cell migration / 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 / RHO GTPases activate PKNs / skeletal muscle tissue development / 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 / guanyl-nucleotide exchange factor activity / 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 / cellular response to ionizing radiation / regulation of cell growth / regulation of actin cytoskeleton organization / neuron migration Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Garcia, C. / Petit, P. / Boutin, J.A. / Ferry, G. / Vuillard, L. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 Title: A structural study of the complex between neuroepithelial cell transforming gene 1 (Net1) and RhoA reveals a potential anticancer drug hot spot. Authors: Petit, A.P. / Garcia-Petit, C. / Bueren-Calabuig, J.A. / Vuillard, L.M. / Ferry, G. / Boutin, J.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4xh9.cif.gz | 448.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4xh9.ent.gz | 367.1 KB | Display | PDB format |
PDBx/mmJSON format | 4xh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/4xh9 ftp://data.pdbj.org/pub/pdb/validation_reports/xh/4xh9 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1xcgS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 42232.383 Da / Num. of mol.: 2 / Fragment: UNP residues 149-501 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NET1, ARHGEF8 / Plasmid: pET28 / Production host: Escherichia coli DH1 (bacteria) / References: UniProt: Q7Z628 #2: Protein | Mass: 20289.164 Da / Num. of mol.: 2 / Fragment: UNP residues 2-180 / Mutation: F25N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARH12, ARHA, RHO12 / Plasmid: pET28 / Production host: Escherichia coli DH1 (bacteria) / References: UniProt: P61586 #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.86 % / Description: PLATE |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M bisTris propane pH7.5, 20% PEG3350, 0.2M Tripotassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2→35 Å / Num. obs: 83900 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Rsym value: 0.06 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.9 / % possible all: 90.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XCG Resolution: 2→34.688 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.09 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→34.688 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 15.1614 Å / Origin y: -20.6284 Å / Origin z: 27.6962 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |