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Yorodumi- PDB-1shz: Crystal Structure of the p115RhoGEF rgRGS Domain in A Complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1shz | ||||||
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Title | Crystal Structure of the p115RhoGEF rgRGS Domain in A Complex with Galpha(13):Galpha(i1) Chimera | ||||||
Components |
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Keywords | SIGNALING PROTEIN / SIGNAL TRANSDUCTION / PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information D5 dopamine receptor binding / CDC42 GTPase cycle / regulation of fibroblast migration / Thromboxane signalling through TP receptor / NRAGE signals death through JNK / Thrombin signalling through proteinase activated receptors (PARs) / RAC1 GTPase cycle / Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / G alpha (12/13) signalling events ...D5 dopamine receptor binding / CDC42 GTPase cycle / regulation of fibroblast migration / Thromboxane signalling through TP receptor / NRAGE signals death through JNK / Thrombin signalling through proteinase activated receptors (PARs) / RAC1 GTPase cycle / Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / G alpha (12/13) signalling events / negative regulation of vascular associated smooth muscle cell migration / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / GTPase activating protein binding / negative regulation of synaptic transmission / G alpha (i) signalling events / regulation of small GTPase mediated signal transduction / branching involved in blood vessel morphogenesis / RHOB GTPase cycle / NRAGE signals death through JNK / RHOC GTPase cycle / negative regulation of vascular associated smooth muscle cell proliferation / Rho protein signal transduction / RHOA GTPase cycle / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cellular response to forskolin / 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 / GDP binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / melanosome / cell cortex / regulation of cell shape / midbody / positive regulation of cytosolic calcium ion concentration / angiogenesis / in utero embryonic development / cell differentiation / intracellular signal transduction / cell cycle / G protein-coupled receptor signaling pathway / cell division / GTPase activity / centrosome / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Chen, Z. / Singer, W.D. / Sternweis, P.C. / Sprang, S.R. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2005 Title: Structure of the p115RhoGEF rgRGS domain-Galpha13/i1 chimera complex suggests convergent evolution of a GTPase activator. Authors: Chen, Z. / Singer, W.D. / 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 | 1shz.cif.gz | 226.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1shz.ent.gz | 179.2 KB | Display | PDB format |
PDBx/mmJSON format | 1shz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1shz_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1shz_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1shz_validation.xml.gz | 41.1 KB | Display | |
Data in CIF | 1shz_validation.cif.gz | 55.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/1shz ftp://data.pdbj.org/pub/pdb/validation_reports/sh/1shz | HTTPS FTP |
-Related structure data
Related structure data | 1agrS 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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2 |
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3 |
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Unit cell |
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Details | The deposited PDB file contains a pair of homodimers of the complexes. However, the biological unit is identical to the monomeric form of the complex |
-Components
-Protein , 2 types, 4 molecules ADCF
#1: Protein | Mass: 39640.191 Da / Num. of mol.: 2 Fragment: residues 21-47, 185-210, 213-230, 240-353 of Galpha(i1) and residues 64-207, 234-235, 254-262 of Galpha(13) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Mus musculus (house mouse) Genus: Mus, Rattus / Species: , / Strain: , / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P10824, UniProt: P27601 #2: Protein | Mass: 26346.879 Da / Num. of mol.: 2 Fragment: N-terminal RhoGEF RGS (rgRGS) domain of p115RhoGEF (residues 7-239) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTrcC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92888 |
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-Non-polymers , 4 types, 90 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 3.14 Å3/Da / Density % sol: 60.52 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Ammonium Sulfate, Tris, Ethylene glycol , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 7, 2003 / Details: MIRRORS |
Radiation | Monochromator: Double crystal, Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 33997 / Num. obs: 31348 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 47 Å2 / Rsym value: 0.188 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 2286 / Rsym value: 0.585 / % possible all: 67.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AGR, CHAIN A Resolution: 2.85→46.49 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1865632.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.4754 Å2 / ksol: 0.30693 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.85→46.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→3.03 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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