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Yorodumi- PDB-1fqj: CRYSTAL STRUCTURE OF THE HETEROTRIMERIC COMPLEX OF THE RGS DOMAIN... -
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-Basic information
Entry | Database: PDB / ID: 1fqj | ||||||
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Title | CRYSTAL STRUCTURE OF THE HETEROTRIMERIC COMPLEX OF THE RGS DOMAIN OF RGS9, THE GAMMA SUBUNIT OF PHOSPHODIESTERASE AND THE GT/I1 CHIMERA ALPHA SUBUNIT [(RGS9)-(PDEGAMMA)-(GT/I1ALPHA)-(GDP)-(ALF4-)-(MG2+)] | ||||||
Components |
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Keywords | SIGNALING PROTEIN / RGS9 / transducin / effector / PDEgamma / G Protein / Phototransduction / rod / RGS / phosphodiesterase / GAP | ||||||
Function / homology | Function and homology information Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / negative regulation of cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-GMP phosphodiesterase / G protein-coupled receptor complex / positive regulation of G protein-coupled receptor signaling pathway / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / regulation of G protein-coupled receptor signaling pathway / ion binding ...Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / negative regulation of cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-GMP phosphodiesterase / G protein-coupled receptor complex / positive regulation of G protein-coupled receptor signaling pathway / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / regulation of G protein-coupled receptor signaling pathway / ion binding / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (i) signalling events / negative regulation of synaptic transmission / acyl binding / response to stimulus / GTPase activating protein binding / Ca2+ pathway / positive regulation of epidermal growth factor receptor signaling pathway / photoreceptor outer segment membrane / G alpha (i) signalling events / 3',5'-cyclic-GMP phosphodiesterase activity / response to light stimulus / phototransduction / cGMP binding / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / negative regulation of signal transduction / regulation of mitotic spindle organization / cellular response to forskolin / visual perception / photoreceptor inner segment / GTPase activator activity / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / photoreceptor disc membrane / GDP binding / heterotrimeric G-protein complex / cell cortex / midbody / positive regulation of MAPK cascade / molecular adaptor activity / neuron projection / intracellular signal transduction / cell cycle / G protein-coupled receptor signaling pathway / cell division / GTPase activity / centrosome / GTP binding / protein kinase binding / magnesium ion binding / protein-containing complex / zinc ion binding / metal ion binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.02 Å | ||||||
Authors | Slep, K.C. / Kercher, M.A. / He, W. / Cowan, C.W. / Wensel, T.G. / Sigler, P.B. | ||||||
Citation | Journal: Nature / Year: 2001 Title: Structural determinants for regulation of phosphodiesterase by a G protein at 2.0 A. Authors: Slep, K.C. / Kercher, M.A. / He, W. / Cowan, C.W. / Wensel, T.G. / Sigler, P.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fqj.cif.gz | 213 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fqj.ent.gz | 169 KB | Display | PDB format |
PDBx/mmJSON format | 1fqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/1fqj ftp://data.pdbj.org/pub/pdb/validation_reports/fq/1fqj | 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
-Protein , 2 types, 4 molecules ADBE
#1: Protein | Mass: 37361.656 Da / Num. of mol.: 2 Fragment: UNP P04695 residues 26-215 and 295-350 linked via UNP P10824 residues 220-298 Source method: isolated from a genetically manipulated source Details: THE CHIMERA COMPRISES RESIDUES 26 TO 215 OF BOVINE GT, RESIDUES 220 TO 298 OF RAT GI1, AND RESIDUES 295 TO 350 OF BOVINE GT Source: (gene. exp.) Bos taurus (cattle), (gene. exp.) Rattus norvegicus (Norway rat) Genus: Bos, Rattus / Species: , / Gene: GNAT1, Gnai1, Gnai-1 / Plasmid: PHIS6(T7) / Production host: Escherichia coli (E. coli) / References: UniProt: P04695, UniProt: P10824 #2: Protein | Mass: 17419.176 Da / Num. of mol.: 2 / Fragment: RGS DOMAIN UNP RESIDUES 276-422 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: RGS9 / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: O46469 |
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-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 4559.094 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 46-87 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: PDE6G, PDEG / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) References: UniProt: P04972, 3',5'-cyclic-GMP phosphodiesterase |
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-Non-polymers , 4 types, 362 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: 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 Å3/Da / Density % sol: 59 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 15.0% PEG8000, 200mM Tris pH9.0, 0.2% beta-ME, 1mM (NH4)2WS4, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 |
Detector | Type: APS-1 / Detector: CCD / Date: Sep 6, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→50 Å / Num. all: 2227054 / Num. obs: 93531 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 8.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.02→2.09 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.553 / Num. unique all: 2094 / % possible all: 99.7 |
Reflection | *PLUS Num. measured all: 2227054 / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS % possible obs: 99.7 % / Mean I/σ(I) obs: 4.4 |
-Processing
Software |
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Refinement | Resolution: 2.02→50 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2012134.44 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / 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: 35.33 Å2 / ksol: 0.344 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.02→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.15 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 9.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 33.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.342 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.306 / Rfactor obs: 0.319 |