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Yorodumi- PDB-3kz1: Crystal Structure of the Complex of PDZ-RhoGEF DH/PH domains with... -
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-Basic information
Entry | Database: PDB / ID: 3kz1 | ||||||
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Title | Crystal Structure of the Complex of PDZ-RhoGEF DH/PH domains with GTP-gamma-S Activated RhoA | ||||||
Components |
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Keywords | SIGNALING PROTEIN / regulation of RhoA GTPase / RhoGEF / DH / PH / Rho / GTPase activation / Guanine-nucleotide releasing factor / Membrane / Cytoskeleton / GTP-binding / Magnesium / Nucleotide-binding / Prenylation / Proto-oncogene | ||||||
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 / cellular response to chemokine / negative regulation of cell migration involved in sprouting angiogenesis / beta selection / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / negative regulation of cell size / RHO GTPases Activate ROCKs / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases activate CIT / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / positive regulation of podosome assembly / negative regulation of cell-substrate adhesion / Wnt signaling pathway, planar cell polarity pathway / regulation of small GTPase mediated signal transduction / Sema4D mediated inhibition of cell attachment and migration / ossification involved in bone maturation / positive regulation of alpha-beta T cell differentiation / odontogenesis / motor neuron apoptotic process / wound healing, spreading of cells / PI3K/AKT activation / positive regulation of leukocyte adhesion to vascular endothelial cell / apical junction complex / regulation of focal adhesion assembly / negative chemotaxis / myosin binding / RHOB GTPase cycle / establishment of cell polarity / NRAGE signals death through JNK / EPHA-mediated growth cone collapse / stress fiber assembly / regulation of neuron projection development / RHOC GTPase cycle / androgen receptor signaling pathway / positive regulation of cytokinesis / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / CDC42 GTPase cycle / Rho protein signal transduction / ficolin-1-rich granule membrane / mitotic spindle assembly / RHOA GTPase cycle / striated muscle contraction / endothelial cell migration / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / regulation of microtubule cytoskeleton organization / cytoplasmic microtubule organization / skeletal muscle tissue development / regulation of cell migration / negative regulation of reactive oxygen species biosynthetic process / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / GTPase activator activity / substrate adhesion-dependent cell spreading / guanyl-nucleotide exchange factor activity / cell-matrix adhesion / small monomeric GTPase / G protein activity / secretory granule membrane / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / G protein-coupled receptor binding / cell periphery / RHO GTPases Activate Formins Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Chen, Z. / Sternweis, P.C. / Sprang, S.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Activated RhoA binds to the pleckstrin homology (PH) domain of PDZ-RhoGEF, a potential site for autoregulation. Authors: Chen, Z. / Medina, F. / Liu, M.Y. / Thomas, C. / Sprang, S.R. / Sternweis, P.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kz1.cif.gz | 231.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kz1.ent.gz | 183.1 KB | Display | PDB format |
PDBx/mmJSON format | 3kz1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/3kz1 ftp://data.pdbj.org/pub/pdb/validation_reports/kz/3kz1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 44568.336 Da / Num. of mol.: 2 / Fragment: UNP residues 710-1085 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF11, KIAA0380 / Plasmid: pGEX-kG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15085 #2: Protein | Mass: 20524.510 Da / Num. of mol.: 2 / Fragment: UNP residues 1-181 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARH12, ARHA, RHO12 / Plasmid: pGEX-kG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61586 #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: 2.92 Å3/Da / Density % sol: 57.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 14-16% PEG 10000, 0.1M ammonium acetate, 0.1M Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 21, 2009 / Details: mirrors |
Radiation | Monochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 38512 / % possible obs: 90.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 62 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 1.46 / % possible all: 62.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 1A2B, 1XCG Resolution: 2.7→33.45 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.905 / SU ML: 0.389 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.789 / ESU R Free: 0.395 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: B-factors reported represent the sum of TLS and residual B-factors
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.317 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→33.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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