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Open data
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Basic information
Entry | Database: PDB / ID: 1a2b | ||||||
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Title | HUMAN RHOA COMPLEXED WITH GTP ANALOGUE | ||||||
![]() | TRANSFORMING PROTEIN RHOA | ||||||
![]() | ONCOGENE PROTEIN / SMALL G-PROTEIN / SIGNAL TRANSDUCTION / GTPASE / RAS SUPERFAMILY | ||||||
Function / homology | ![]() 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 / androgen receptor signaling pathway / positive regulation of cytokinesis / 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 / 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ihara, K. / Muraguchi, S. / Kato, M. / Shimizu, T. / Shirakawa, M. / Kuroda, S. / Kaibuchi, K. / Hakoshima, T. | ||||||
![]() | ![]() Title: Crystal structure of human RhoA in a dominantly active form complexed with a GTP analogue. Authors: Ihara, K. / Muraguchi, S. / Kato, M. / Shimizu, T. / Shirakawa, M. / Kuroda, S. / Kaibuchi, K. / Hakoshima, T. #1: ![]() Title: Refined Crystal Structure of the Triphosphate Conformation of H-Ras P21 at 1.35 A Resolution: Implications for the Mechanism of GTP Hydrolysis Authors: Pai, E.F. / Krengel, U. / Petsko, G.A. / Goody, R.S. / Kabsch, W. / Wittinghofer, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.8 KB | Display | ![]() |
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PDB format | ![]() | 35.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 712.7 KB | Display | ![]() |
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Full document | ![]() | 714.7 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 12.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5p21S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20596.615 Da / Num. of mol.: 1 / Fragment: RESIDUES 1 - 181 Mutation: G14V, RESIDUES 1 - 181 WERE CLONED, THE N-TERMINUS CONTAINS A HIS-TAG Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH ONE GTPGAMMAS AND ONE MG ION / Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GSP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: CRYSTALS WERE OBTAINED AT 277 K BY THE HANGING-DROP VAPOR DIFFUSION METHOD FROM SOLUTIONS CONTAINING 10 MG/ML(PROTEIN,GTPGAMMAS,MG2+ MIXTURE), 10% PEG 8000,7.5% 14-DIOXANE, 50 MM TRIS-HCL PH ...Details: CRYSTALS WERE OBTAINED AT 277 K BY THE HANGING-DROP VAPOR DIFFUSION METHOD FROM SOLUTIONS CONTAINING 10 MG/ML(PROTEIN,GTPGAMMAS,MG2+ MIXTURE), 10% PEG 8000,7.5% 14-DIOXANE, 50 MM TRIS-HCL PH 8.5, EQUILIBRATED AGAINST 20% PEG 8000,15% 14-DIOXANE, 100 MM TRIS-HCL PH 8.5, vapor diffusion - hanging drop PH range: 7.5-8.5 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 1, 1997 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.4 Å / Num. obs: 8683 / % possible obs: 89.3 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.0875 / Net I/σ(I): 7.91 |
Reflection shell | Resolution: 2.4→2.5 Å / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 2.04 / % possible all: 74.8 |
Reflection | *PLUS Num. measured all: 61579 |
Reflection shell | *PLUS % possible obs: 74.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 5P21 Resolution: 2.4→15 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.0001 / Cross valid method: THROUGHOUT / σ(F): 1
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Displacement parameters | Biso mean: 43.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.51 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.306 |