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Yorodumi- PDB-5jcp: RhoGAP domain of ARAP3 in complex with RhoA in the transition state -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jcp | ||||||
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Title | RhoGAP domain of ARAP3 in complex with RhoA in the transition state | ||||||
Components | Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3,Linker,Transforming protein RhoA | ||||||
Keywords | SIGNALING PROTEIN / HYDROLASE / RhoA / RhoGAP / ARAP3 | ||||||
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 / phosphatidylinositol-3,4-bisphosphate binding / 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 / phosphatidylinositol-3,4,5-trisphosphate binding / cleavage furrow / CDC42 GTPase cycle / 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 / RAC3 GTPase cycle / 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 / vesicle-mediated transport / positive regulation of stress fiber assembly / cytoskeleton organization / GPVI-mediated activation cascade / ruffle / EPHB-mediated forward signaling / RAC1 GTPase cycle / 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Bao, H. / Li, F. / Wang, C. / Wang, N. / Jiang, Y. / Tang, Y. / Wu, J. / Shi, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural Basis for the Specific Recognition of RhoA by the Dual GTPase-activating Protein ARAP3 Authors: Bao, H. / Li, F. / Wang, C. / Wang, N. / Jiang, Y. / Tang, Y. / Wu, J. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jcp.cif.gz | 304.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jcp.ent.gz | 242.3 KB | Display | PDB format |
PDBx/mmJSON format | 5jcp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jcp_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5jcp_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5jcp_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 5jcp_validation.cif.gz | 39 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/5jcp ftp://data.pdbj.org/pub/pdb/validation_reports/jc/5jcp | HTTPS FTP |
-Related structure data
Related structure data | 5jd0SC 1a2bS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 47132.617 Da / Num. of mol.: 2 / Fragment: UNP residues 906-1107,UNP residues 2-181 / Mutation: F25N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others) Gene: ARAP3, RHOA Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q8WWN8, UniProt: P61586 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.31 Å3/Da / Density % sol: 46.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100 mM MES, 15%(v/v) PEG 550 MME, 4%(v/v) Acetone |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 27, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. obs: 52079 / % possible obs: 99.8 % / Redundancy: 6 % / Biso Wilson estimate: 30.96 Å2 / Rmerge(I) obs: 0.108 / Net I/av σ(I): 15.922 / Net I/σ(I): 9.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JD0, 1A2B Resolution: 2.1→46.711 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.85 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.711 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 10.869 Å / Origin y: -3.4692 Å / Origin z: 18.0172 Å
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Refinement TLS group | Selection details: all |