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Yorodumi- PDB-6v6v: Crystal structure of oncogenic RhoA mutant G14V complexed with GDP -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v6v | ||||||
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Title | Crystal structure of oncogenic RhoA mutant G14V complexed with GDP | ||||||
Components | Transforming protein RhoA | ||||||
Keywords | HYDROLASE / GTPase / Switch I / Switch II | ||||||
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 / cerebral cortex cell migration / negative regulation of cell migration involved in sprouting angiogenesis / cellular response to chemokine / beta selection / establishment of epithelial cell apical/basal polarity / negative regulation of cell size / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / ERBB2 Regulates Cell Motility / 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 focal adhesion assembly / negative chemotaxis / myosin binding / EPHA-mediated growth cone collapse / stress fiber assembly / regulation of neuron projection development / RHOC GTPase cycle / positive regulation of cytokinesis / androgen receptor signaling pathway / cellular response to cytokine stimulus / 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 / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / regulation of cell migration / 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 / ruffle membrane / neuron migration / positive regulation of protein serine/threonine kinase activity / cell morphogenesis / positive regulation of non-canonical NF-kappaB signal transduction / cytoplasmic side of plasma membrane / VEGFA-VEGFR2 Pathway / G beta:gamma signalling through PI3Kgamma / cell junction Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å | ||||||
Authors | Lin, Y. / Zheng, Y. | ||||||
Citation | Journal: Structure / Year: 2021 Title: Structure of an inactive conformation of GTP-bound RhoA GTPase. Authors: Lin, Y. / Lu, S. / Zhang, J. / Zheng, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v6v.cif.gz | 100.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v6v.ent.gz | 72.6 KB | Display | PDB format |
PDBx/mmJSON format | 6v6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v6v_validation.pdf.gz | 344.8 KB | Display | wwPDB validaton report |
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Full document | 6v6v_full_validation.pdf.gz | 344.8 KB | Display | |
Data in XML | 6v6v_validation.xml.gz | 1.4 KB | Display | |
Data in CIF | 6v6v_validation.cif.gz | 4.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/6v6v ftp://data.pdbj.org/pub/pdb/validation_reports/v6/6v6v | HTTPS FTP |
-Related structure data
Related structure data | 6v6mC 6v6uC 1ftnS 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: 20620.596 Da / Num. of mol.: 1 / Fragment: C-terminal trancated at residue 181 / Mutation: G14V, F25N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARH12, ARHA, RHO12 / Plasmid: pGEX-2T / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61586, small monomeric GTPase | ||||
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#2: Chemical | ChemComp-GDP / | ||||
#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.64 % / Mosaicity: 0.02 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 20-24% PEG8K, 15% Dioxane, 0.1M Tris pH8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Kohzu HLD-4 Double Crystal water cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→25.817 Å / Num. all: 36248 / Num. obs: 36248 / % possible obs: 98.8 % / Redundancy: 3.6 % / Rpim(I) all: 0.168 / Rrim(I) all: 0.326 / Rsym value: 0.237 / Net I/av σ(I): 1.4 / Net I/σ(I): 2.8 / Num. measured all: 131266 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdbid 1FTN Resolution: 1.4→24.45 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.54 Å2 / Biso mean: 29.248 Å2 / Biso min: 8.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→24.45 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: 3.5724 Å / Origin y: 2.9723 Å / Origin z: 1.9617 Å
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Refinement TLS group |
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