[English] 日本語
Yorodumi- PDB-3ah8: Structure of heterotrimeric G protein Galpha-q beta gamma in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ah8 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of heterotrimeric G protein Galpha-q beta gamma in complex with an inhibitor YM-254890 | |||||||||
Components |
| |||||||||
Keywords | SIGNALING PROTEIN/INHIBITOR / Heterotrimeric G protein / GTPase / Galpha-q / Gbeta / Ggamma / Inhibitor / YM-254890 / SIGNALING PROTEIN / SIGNALING PROTEIN-INHIBITOR complex | |||||||||
Function / homology | Function and homology information Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / PLC beta mediated events / forebrain neuron development / regulation of melanocyte differentiation / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / Thrombin signalling through proteinase activated receptors (PARs) / Extra-nuclear estrogen signaling / G-protein activation ...Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / PLC beta mediated events / forebrain neuron development / regulation of melanocyte differentiation / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / Thrombin signalling through proteinase activated receptors (PARs) / Extra-nuclear estrogen signaling / G-protein activation / Adenylate cyclase inhibitory pathway / G alpha (q) signalling events / endothelin receptor signaling pathway / ion channel modulating, G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / Olfactory Signaling Pathway / developmental pigmentation / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / phospholipase C-activating dopamine receptor signaling pathway / cranial skeletal system development / ADP signalling through P2Y purinoceptor 1 / regulation of platelet activation / Activation of the phototransduction cascade / maternal behavior / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / glutamate receptor signaling pathway / GTPase activating protein binding / negative regulation of synaptic transmission / G alpha (i) signalling events / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / alkylglycerophosphoethanolamine phosphodiesterase activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / G alpha (q) signalling events / neurotransmitter receptor localization to postsynaptic specialization membrane / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / embryonic digit morphogenesis / neuron remodeling / Vasopressin regulates renal water homeostasis via Aquaporins / action potential / ligand-gated ion channel signaling pathway / negative regulation of potassium ion transport / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / enzyme regulator activity / regulation of mitotic spindle organization / cellular response to forskolin / GTPase activator activity / positive regulation of smooth muscle cell proliferation / G protein activity / post-embryonic development / skeletal system development / caveola / G protein-coupled receptor binding / regulation of blood pressure / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / photoreceptor disc membrane / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / GDP binding / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / heart development / phospholipase C-activating G protein-coupled receptor signaling pathway / cell cortex / midbody / cell body / nuclear membrane / postsynapse / G protein-coupled receptor signaling pathway / cell division / GTPase activity Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) Mus musculus (house mouse) Bos taurus (cattle) Chromobacterium sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Nishimura, A. / Kitano, K. / Takasaki, J. / Taniguchi, M. / Mizuno, N. / Tago, K. / Hakoshima, T. / Itoh, H. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structural basis for the specific inhibition of heterotrimeric Gq protein by a small molecule. Authors: Nishimura, A. / Kitano, K. / Takasaki, J. / Taniguchi, M. / Mizuno, N. / Tago, K. / Hakoshima, T. / Itoh, H. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ah8.cif.gz | 159.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ah8.ent.gz | 120.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ah8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ah8_validation.pdf.gz | 798.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ah8_full_validation.pdf.gz | 826.5 KB | Display | |
Data in XML | 3ah8_validation.xml.gz | 30.1 KB | Display | |
Data in CIF | 3ah8_validation.cif.gz | 40 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/3ah8 ftp://data.pdbj.org/pub/pdb/validation_reports/ah/3ah8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 41427.027 Da / Num. of mol.: 1 Fragment: UNP entry P10824 residues 2-28, UNP entry P21279 residues 37-359 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Mus musculus (house mouse) Gene: gmhB / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five cell / References: UniProt: P10824, UniProt: P21279 |
---|---|
#2: Protein | Mass: 37416.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GNB1 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five cell / References: UniProt: P62871 |
#3: Protein | Mass: 8592.894 Da / Num. of mol.: 1 / Mutation: C68S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GNG2 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five cell / References: UniProt: P63212 |
#4: Protein/peptide | |
#5: Chemical | ChemComp-GDP / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.5 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.1 Details: 7% PEG 4000, 30% (v/v) glycerol, 70 mM acetate-NaOH, pH 5.1, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 24, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. obs: 19018 / % possible obs: 94.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.059 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 2.4 / % possible all: 76.9 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2BCJ and 1GP2 Resolution: 2.9→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT
| ||||||||||||||||||||
Displacement parameters | Biso mean: 91.53 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
| ||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3 Å /
|