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Yorodumi- PDB-2ihb: Crystal structure of the heterodimeric complex of human RGS10 and... -
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-Basic information
Entry | Database: PDB / ID: 2ihb | ||||||
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Title | Crystal structure of the heterodimeric complex of human RGS10 and activated Gi alpha 3 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / G protein signalling / RGS / heterotrimeric G protein / signalling complex / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information negative regulation of adenylate cyclase activity / regulation of G protein-coupled receptor signaling pathway / GTP metabolic process / dopamine receptor signaling pathway / positive regulation of macroautophagy / Adenylate cyclase inhibitory pathway / G-protein alpha-subunit binding / axon terminus / negative regulation of signal transduction / response to amphetamine ...negative regulation of adenylate cyclase activity / regulation of G protein-coupled receptor signaling pathway / GTP metabolic process / dopamine receptor signaling pathway / positive regulation of macroautophagy / Adenylate cyclase inhibitory pathway / G-protein alpha-subunit binding / axon terminus / negative regulation of signal transduction / response to amphetamine / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / GTPase activator activity / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G protein-coupled acetylcholine receptor signaling pathway / ADP signalling through P2Y purinoceptor 12 / positive regulation of GTPase activity / G alpha (z) signalling events / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / GDP binding / heterotrimeric G-protein complex / midbody / G alpha (i) signalling events / G alpha (s) signalling events / dendritic spine / Extra-nuclear estrogen signaling / nuclear body / cell cycle / G protein-coupled receptor signaling pathway / cell division / lysosomal membrane / GTPase activity / centrosome / neuronal cell body / synapse / GTP binding / nucleolus / Golgi apparatus / extracellular exosome / nucleoplasm / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | ||||||
Authors | Soundararajan, M. / Turnbull, A.P. / Papagrigoriou, E. / Pike, A.C.W. / Bunkoczi, G. / Ugochukwu, E. / Gorrec, F. / von Delft, F. / Weigelt, J. / Edwards, A. ...Soundararajan, M. / Turnbull, A.P. / Papagrigoriou, E. / Pike, A.C.W. / Bunkoczi, G. / Ugochukwu, E. / Gorrec, F. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Doyle, D.A. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Structural diversity in the RGS domain and its interaction with heterotrimeric G protein alpha-subunits. Authors: Soundararajan, M. / Willard, F.S. / Kimple, A.J. / Turnbull, A.P. / Ball, L.J. / Schoch, G.A. / Gileadi, C. / Fedorov, O.Y. / Dowler, E.F. / Higman, V.A. / Hutsell, S.Q. / Sundstrom, M. / ...Authors: Soundararajan, M. / Willard, F.S. / Kimple, A.J. / Turnbull, A.P. / Ball, L.J. / Schoch, G.A. / Gileadi, C. / Fedorov, O.Y. / Dowler, E.F. / Higman, V.A. / Hutsell, S.Q. / Sundstrom, M. / Doyle, D.A. / Siderovski, D.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ihb.cif.gz | 101.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ihb.ent.gz | 74.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ihb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/2ihb ftp://data.pdbj.org/pub/pdb/validation_reports/ih/2ihb | HTTPS FTP |
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-Related structure data
Related structure data | 1zv4C 2a72C 2af0C 2bt2C 2bv1SC 2es0C 2gtpC 2i59C 2ihdC 2ik8C 2jm5C 2jnuC 2odeC 2owiC 1agrS 1eztS 1ezyS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 37201.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)R3 / References: UniProt: P08754 |
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#2: Protein | Mass: 18021.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RGS10 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)R3 / References: UniProt: Q96GN0, UniProt: O43665*PLUS |
-Non-polymers , 4 types, 21 molecules
#3: Chemical | ChemComp-ALF / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-GDP / |
#6: 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: 3.33 Å3/Da / Density % sol: 63.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2M (NH4)2SO4, 0.1M Bis-Tris, pH 5.5, 25% PEG3350 , VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97925 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 6, 2006 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97925 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 20815 / Num. obs: 20470 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.7→2.75 Å / % possible all: 80.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Swissmodel based on the coordinates of PDB entries 1agr, 1ezt, 1ezy, 2bv1 Resolution: 2.71→47.6 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.933 / SU B: 21.321 / SU ML: 0.211 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.452 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.111 Å2
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Refinement step | Cycle: LAST / Resolution: 2.71→47.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.71→2.777 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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