+Open data
-Basic information
Entry | Database: PDB / ID: 7wza | ||||||
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Title | An open conformation Form 1 of switch II for RhoA | ||||||
Components | Transforming protein RhoA | ||||||
Keywords | CELL INVASION / small GTPase / Rho family | ||||||
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 / 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 / positive regulation of cytokinesis / cerebral cortex cell migration / androgen receptor signaling pathway / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.50028778245 Å | ||||||
Authors | Jiang, H. / Luo, C. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2023 Title: A RhoA structure with switch II flipped outward revealed the conformational dynamics of switch II region. Authors: Jiang, H. / Zu, S. / Lu, Y. / Sun, Z. / Adeerjiang, A. / Guo, Q. / Zhang, H. / Dong, C. / Wu, Q. / Ding, H. / Du, D. / Wang, M. / Liu, C. / Tang, Y. / Liang, Z. / Luo, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wza.cif.gz | 70.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wza.ent.gz | 39.2 KB | Display | PDB format |
PDBx/mmJSON format | 7wza.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wza_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7wza_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7wza_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 7wza_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/7wza ftp://data.pdbj.org/pub/pdb/validation_reports/wz/7wza | HTTPS FTP |
-Related structure data
Related structure data | 7wzcC 1ftnS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20936.857 Da / Num. of mol.: 1 / Mutation: C16V,C20S,C83V,C159T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARH12, ARHA, RHO12 / Production host: Escherichia coli (E. coli) / References: UniProt: P61586, small monomeric GTPase |
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#2: Chemical | ChemComp-GDP / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.92 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2M potassium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9875 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9875 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→33.684 Å / Num. obs: 28558 / % possible obs: 99.8 % / Redundancy: 12.2 % / Biso Wilson estimate: 14.016308064 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rpim(I) all: 0.036 / Rrim(I) all: 0.128 / Net I/σ(I): 23.15 |
Reflection shell | Resolution: 1.5→1.554 Å / Num. unique obs: 2367 / CC1/2: 0.72 / CC star: 0.915 / Rpim(I) all: 0.403 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FTN Resolution: 1.50028778245→33.684 Å / SU ML: 0.14119592103 / Cross valid method: FREE R-VALUE / σ(F): 1.34750913974 / Phase error: 21.1541754864 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 19.0578590928 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.50028778245→33.684 Å
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Refine LS restraints |
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LS refinement shell |
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