+Open data
-Basic information
Entry | Database: PDB / ID: 3tvd | ||||||
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Title | Crystal Structure of Mouse RhoA-GTP complex | ||||||
Components | Transforming protein RhoA | ||||||
Keywords | SIGNALING PROTEIN / Alpha helical / Protein_GTP complex / Helical protein / GTP binding protein / Regulates signal transduction pathway / GTP / Nil / Membrane | ||||||
Function / homology | Function and homology information trabecula morphogenesis / EPHA-mediated growth cone collapse / PCP/CE pathway / RHO GTPases activate PKNs / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / : / Sema4D mediated inhibition of cell attachment and migration / RHO GTPases Activate ROCKs / ERBB2 Regulates Cell Motility ...trabecula morphogenesis / EPHA-mediated growth cone collapse / PCP/CE pathway / RHO GTPases activate PKNs / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / : / Sema4D mediated inhibition of cell attachment and migration / RHO GTPases Activate ROCKs / ERBB2 Regulates Cell Motility / RHO GTPases activate KTN1 / GPVI-mediated activation cascade / PI3K/AKT activation / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Sema4D induced cell migration and growth-cone collapse / Ovarian tumor domain proteases / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / VEGFA-VEGFR2 Pathway / RHO GTPases Activate Formins / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / G alpha (12/13) signalling events / : / RHO GTPases activate CIT / : / regulation of actin polymerization or depolymerization / regulation of dendrite development / response to xenobiotic stimulus => GO:0009410 / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / regulation of modification of synaptic structure / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / cellular response to progesterone stimulus / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / regulation of neural precursor cell proliferation / cleavage furrow formation / EPHB-mediated forward signaling / regulation of modification of postsynaptic actin cytoskeleton / cortical cytoskeleton organization / positive regulation of smooth muscle contraction / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / cell junction assembly / apical junction assembly / regulation of systemic arterial blood pressure by endothelin / G beta:gamma signalling through PI3Kgamma / cellular response to chemokine / negative regulation of cell migration involved in sprouting angiogenesis / beta selection / establishment of epithelial cell apical/basal polarity / negative regulation of cell size / negative regulation of oxidative phosphorylation / apolipoprotein A-I-mediated signaling pathway / GTP metabolic process / positive regulation of podosome assembly / negative regulation of cell-substrate adhesion / ossification involved in bone maturation / positive regulation of alpha-beta T cell differentiation / odontogenesis / wound healing, spreading of cells / Neutrophil degranulation / positive regulation of leukocyte adhesion to vascular endothelial cell / apical junction complex / negative chemotaxis / myosin binding / Rho GDP-dissociation inhibitor binding / stress-activated protein kinase signaling cascade / positive regulation of actin filament polymerization / stress fiber assembly / regulation of neuron projection development / androgen receptor signaling pathway / positive regulation of cytokinesis / cellular response to cytokine stimulus / cerebral cortex cell migration / cleavage furrow / regulation of calcium ion transport / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / Rho protein signal transduction / mitotic spindle assembly / negative regulation of neuron differentiation / positive regulation of cell adhesion / endothelial cell migration / positive regulation of T cell migration / response to amino acid / response to glucose / regulation of microtubule cytoskeleton organization / cytoplasmic microtubule organization / response to mechanical stimulus / skeletal muscle tissue development / negative regulation of canonical NF-kappaB signal transduction / cytoskeleton organization / regulation of cell migration / negative regulation of reactive oxygen species biosynthetic process / positive regulation of vasoconstriction / response to glucocorticoid Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.989 Å | ||||||
Authors | Swaminathan, K. / Pal, K. / Jobichen, C. | ||||||
Citation | Journal: J.Struct.Funct.Genom. / Year: 2012 Title: Crystal structure of mouse RhoA:GTPgammaS complex in a centered lattice. Authors: Jobichen, C. / Pal, K. / Swaminathan, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tvd.cif.gz | 86.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tvd.ent.gz | 64.8 KB | Display | PDB format |
PDBx/mmJSON format | 3tvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/3tvd ftp://data.pdbj.org/pub/pdb/validation_reports/tv/3tvd | HTTPS FTP |
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-Related structure data
Related structure data | 1ftnS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 21813.186 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arha, Arha2, Rhoa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61589 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.2M Ammonium acetate, 0.1M Sodium acetate (pH4.6), 30% Polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 21, 2011 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.989→29 Å / Num. all: 8595 / Num. obs: 8595 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rsym value: 0.16 |
Reflection shell | Resolution: 3→3.15 Å / Redundancy: 4.9 % / Rsym value: 0.34 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FTN Resolution: 2.989→14.999 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 10.69 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.989→14.999 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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