+Open data
-Basic information
Entry | Database: PDB / ID: 6mhe | ||||||
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Title | Galphai3 co-crystallized with KB752 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / exchange / GPCR / inhibitory | ||||||
Function / homology | Function and homology information zymogen granule / Extra-nuclear estrogen signaling / negative regulation of secretion / Adenylate cyclase inhibitory pathway / positive regulation of NAD(P)H oxidase activity / vesicle fusion / ADP signalling through P2Y purinoceptor 12 / G alpha (i) signalling events / GTP metabolic process / GTPase activating protein binding ...zymogen granule / Extra-nuclear estrogen signaling / negative regulation of secretion / Adenylate cyclase inhibitory pathway / positive regulation of NAD(P)H oxidase activity / vesicle fusion / ADP signalling through P2Y purinoceptor 12 / G alpha (i) signalling events / GTP metabolic process / GTPase activating protein binding / dopamine receptor signaling pathway / positive regulation of macroautophagy / negative regulation of apoptotic signaling pathway / G protein-coupled serotonin receptor binding / positive regulation of vascular associated smooth muscle cell proliferation / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / positive regulation of superoxide anion generation / G protein-coupled receptor binding / brain development / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / GDP binding / heterotrimeric G-protein complex / midbody / cell cycle / membrane raft / cell division / protein domain specific binding / Golgi membrane / GTPase activity / centrosome / GTP binding / endoplasmic reticulum membrane / Golgi apparatus / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Rees, S.D. / Kalogriopoulos, N.A. / Ngo, T. / Kopcho, N. / Ilatovskiy, A. / Sun, N. / Komives, E. / Chang, G. / Ghosh, P. / Kufareva, I. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Structural basis for GPCR-independent activation of heterotrimeric Gi proteins. Authors: Kalogriopoulos, N.A. / Rees, S.D. / Ngo, T. / Kopcho, N.J. / Ilatovskiy, A.V. / Sun, N. / Komives, E.A. / Chang, G. / Ghosh, P. / Kufareva, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mhe.cif.gz | 177.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mhe.ent.gz | 113.1 KB | Display | PDB format |
PDBx/mmJSON format | 6mhe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/6mhe ftp://data.pdbj.org/pub/pdb/validation_reports/mh/6mhe | HTTPS FTP |
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-Related structure data
Related structure data | 6mhfC 4g5rS 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: 40066.418 Da / Num. of mol.: 1 / Fragment: residues 26-354 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gnai3, Gnai-3 / Production host: Escherichia coli (E. coli) / References: UniProt: P08753 |
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#2: Protein/peptide | Mass: 2037.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-GDP / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.13 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99999 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→66.91 Å / Num. obs: 44127 / % possible obs: 94 % / Redundancy: 3.7 % / Biso Wilson estimate: 40.57 Å2 / Net I/σ(I): 15.91 |
Reflection shell | Resolution: 2.2→2.27 Å / Num. unique obs: 24419 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4G5R Resolution: 2.2→52.15 Å / SU ML: 0.3027 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 27.3572
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→52.15 Å
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Refine LS restraints |
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LS refinement shell |
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