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Yorodumi- PDB-5kdo: Heterotrimeric complex of the 4 alanine insertion variant of the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kdo | |||||||||||||||
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Title | Heterotrimeric complex of the 4 alanine insertion variant of the Gi alpha1 subunit and the Gbeta1-Ggamma1 | |||||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / Heterotrimeric G protein G protein Coupled Receptors G protein activation G protein structure GDP release | |||||||||||||||
Function / homology | Function and homology information Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / GTPase activating protein binding ...Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / 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 / 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 / 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 / Vasopressin regulates renal water homeostasis via Aquaporins / 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 / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating 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 / cell cortex / midbody / postsynapse / G protein-coupled receptor signaling pathway / cell division / GTPase activity / centrosome / glutamatergic synapse / GTP binding / magnesium ion binding / protein-containing complex / membrane / nucleus / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Rattus norvegicus (Norway rat) Bos taurus (cattle) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||||||||
Authors | Kaya, A.I. / Lokits, A.D. / Gilbert, J. / Iverson, T.M. / Meiler, J. / Hamm, H.E. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: J.Biol.Chem. / Year: 2016 Title: A Conserved Hydrophobic Core in G alpha i1 Regulates G Protein Activation and Release from Activated Receptor. Authors: Kaya, A.I. / Lokits, A.D. / Gilbert, J.A. / Iverson, T.M. / Meiler, J. / Hamm, H.E. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kdo.cif.gz | 164.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kdo.ent.gz | 126.8 KB | Display | PDB format |
PDBx/mmJSON format | 5kdo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kdo_validation.pdf.gz | 803.9 KB | Display | wwPDB validaton report |
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Full document | 5kdo_full_validation.pdf.gz | 810.8 KB | Display | |
Data in XML | 5kdo_validation.xml.gz | 29.8 KB | Display | |
Data in CIF | 5kdo_validation.cif.gz | 42.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/5kdo ftp://data.pdbj.org/pub/pdb/validation_reports/kd/5kdo | HTTPS FTP |
-Related structure data
Related structure data | 5kdlC 1gp2S 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: 40683.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gnai1, Gnai-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P10824 |
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#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: Bos taurus (cattle) / References: UniProt: P62871 |
#3: Protein | Mass: 8556.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GNGT1 / Production host: Bos taurus (cattle) / References: UniProt: P02698 |
#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: 2.69 Å3/Da / Density % sol: 54.25 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 19-24 % PEG 8000, 1-5% 2-propanolol, 1% OG, 100 mM HEPES (pH 7.0) and 100 mM NaOAc (pH 6.4) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.987 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40.248 Å / Num. obs: 71880 / % possible obs: 100 % / Redundancy: 8.5 % / Rsym value: 0.074 / Net I/σ(I): 17.44 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 1.36 / Rsym value: 1.234 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GP2 Resolution: 1.9→40.25 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.87
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→40.25 Å
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Refine LS restraints |
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LS refinement shell |
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