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Yorodumi- PDB-3cx6: Crystal Structure of PDZRhoGEF rgRGS Domain in a Complex with Gal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cx6 | ||||||
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Title | Crystal Structure of PDZRhoGEF rgRGS Domain in a Complex with Galpha-13 Bound to GDP | ||||||
Components |
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Keywords | SIGNALING PROTEIN / SIGNAL TRANSDUCTION / PROTEIN COMPLEX / GTP-binding / Lipoprotein / Membrane / Nucleotide-binding / Palmitate / Phosphoprotein / Transducer / Coiled coil / Cytoplasm / GTPase activation / Guanine-nucleotide releasing factor | ||||||
Function / homology | Function and homology information Sema4D induced cell migration and growth-cone collapse / RHOB GTPase cycle / CDC42 GTPase cycle / D5 dopamine receptor binding / NRAGE signals death through JNK / G alpha (12/13) signalling events / RAC1 GTPase cycle / CDC42 GTPase cycle / regulation of fibroblast migration / Thromboxane signalling through TP receptor ...Sema4D induced cell migration and growth-cone collapse / RHOB GTPase cycle / CDC42 GTPase cycle / D5 dopamine receptor binding / NRAGE signals death through JNK / G alpha (12/13) signalling events / RAC1 GTPase cycle / CDC42 GTPase cycle / regulation of fibroblast migration / Thromboxane signalling through TP receptor / NRAGE signals death through JNK / RHOA GTPase cycle / regulation of postsynapse assembly / Thrombin signalling through proteinase activated receptors (PARs) / RAC1 GTPase cycle / positive regulation of L-glutamate import across plasma membrane / G alpha (12/13) signalling events / negative regulation of vascular associated smooth muscle cell migration / branching involved in blood vessel morphogenesis / negative regulation of vascular associated smooth muscle cell proliferation / Rho protein signal transduction / GTPase activator activity / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / brush border membrane / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / platelet activation / regulation of blood pressure / heterotrimeric G-protein complex / melanosome / regulation of cell shape / positive regulation of cytosolic calcium ion concentration / angiogenesis / in utero embryonic development / postsynapse / cell differentiation / intracellular signal transduction / G protein-coupled receptor signaling pathway / GTPase activity / GTP binding / positive regulation of DNA-templated transcription / membrane / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Sprang, S.R. / Chen, Z. | ||||||
Citation | Journal: Structure / Year: 2008 Title: Recognition of the Activated States of Galpha13 by the rgRGS Domain of PDZRhoGEF. Authors: Chen, Z. / Singer, W.D. / Danesh, S.M. / Sternweis, P.C. / Sprang, S.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cx6.cif.gz | 121.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cx6.ent.gz | 91.2 KB | Display | PDB format |
PDBx/mmJSON format | 3cx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/3cx6 ftp://data.pdbj.org/pub/pdb/validation_reports/cx/3cx6 | HTTPS FTP |
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-Related structure data
Related structure data | 3cx7C 3cx8C 1htjS 1zcbS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39728.543 Da / Num. of mol.: 1 / Fragment: N-terminally truncated Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gna13, Gna-13 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P27601 |
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#2: Protein | Mass: 23323.350 Da / Num. of mol.: 1 / Fragment: RhoGEF-RGS (rgRGS) Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arhgef11 / Plasmid: pGEX-kG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ES67 |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-GDP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 22-27 % polyethylene glycol 4000 and 100 mM Na+ HEPES, pH 7.2-8.1, pH 7.5, 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-ID / Wavelength: 0.97921 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2007 / Details: Mirrors |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→75 Å / Num. obs: 20558 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Biso Wilson estimate: 49.8 Å2 / Rsym value: 0.086 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.574 / % possible all: 83.3 |
-Processing
Software |
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Refinement | Starting model: PDB Entry 1ZCB, 1HTJ Resolution: 2.5→75 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 25.419 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.483 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→75 Å
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Refine LS restraints |
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Xplor file |
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