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Yorodumi- PDB-1svk: Structure of the K180P mutant of Gi alpha subunit bound to AlF4 a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1svk | ||||||
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Title | Structure of the K180P mutant of Gi alpha subunit bound to AlF4 and GDP | ||||||
Components | Guanine nucleotide-binding protein G(i), alpha-1 subunit | ||||||
Keywords | HYDROLASE / SIGNALING PROTEIN / Gi alpha subunit / K180P mutation / Active form | ||||||
Function / homology | Function and homology information Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (i) signalling events / negative regulation of synaptic transmission / GTPase activating protein binding / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding ...Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (i) signalling events / negative regulation of synaptic transmission / GTPase activating protein binding / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / cellular response to forskolin / regulation of mitotic spindle organization / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / GDP binding / heterotrimeric G-protein complex / cell cortex / midbody / G protein-coupled receptor signaling pathway / cell cycle / cell division / GTPase activity / centrosome / GTP binding / magnesium ion binding / protein-containing complex / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Thomas, C.J. / Du, X. / Li, P. / Wang, Y. / Ross, E.M. / Sprang, S.R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Uncoupling conformational change from GTP hydrolysis in a heterotrimeric G protein {alpha}-subunit. Authors: Thomas, C.J. / Du, X. / Li, P. / Wang, Y. / Ross, E.M. / 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 | 1svk.cif.gz | 86.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1svk.ent.gz | 63.1 KB | Display | PDB format |
PDBx/mmJSON format | 1svk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/1svk ftp://data.pdbj.org/pub/pdb/validation_reports/sv/1svk | HTTPS FTP |
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-Related structure data
Related structure data | 1svsC 1gfiS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40235.770 Da / Num. of mol.: 1 / Mutation: K180P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GNAI1, GNAI-1 / Plasmid: pQE-60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM-109 / References: UniProt: P10824, EC: 3.6.1.46 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ALF / |
#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: 2.38 Å3/Da / Density % sol: 48.39 % |
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Crystal grow | Temperature: 293.16 K / pH: 6.5 Details: Ammonium Sulphite, Sodium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.16K, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9784 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2003 |
Radiation | Monochromator: DOUBLE-CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9784 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 24776 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rsym value: 0.073 / Net I/σ(I): 28.5 |
Reflection shell | Highest resolution: 2 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 5.6 / Rsym value: 0.34 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GFI Resolution: 2→20 Å / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 48.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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