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Yorodumi- PDB-2ode: Crystal structure of the heterodimeric complex of human RGS8 and ... -
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-Basic information
Entry | Database: PDB / ID: 2ode | ||||||
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Title | Crystal structure of the heterodimeric complex of human RGS8 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 regulation of dopamine receptor signaling pathway / negative regulation of adenylate cyclase activity / GTP metabolic process / dopamine receptor signaling pathway / neuronal cell body membrane / positive regulation of macroautophagy / Adenylate cyclase inhibitory pathway / negative regulation of signal transduction / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / GTPase activator activity ...regulation of dopamine receptor signaling pathway / negative regulation of adenylate cyclase activity / GTP metabolic process / dopamine receptor signaling pathway / neuronal cell body membrane / positive regulation of macroautophagy / Adenylate cyclase inhibitory pathway / negative regulation of signal transduction / 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 / cytoplasmic side of plasma membrane / G alpha (z) signalling events / positive regulation of GTPase activity / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / GDP binding / heterotrimeric G-protein complex / G alpha (i) signalling events / midbody / perikaryon / G alpha (s) signalling events / Extra-nuclear estrogen signaling / cell cycle / G protein-coupled receptor signaling pathway / lysosomal membrane / cell division / GTPase activity / centrosome / dendrite / synapse / GTP binding / nucleolus / Golgi apparatus / extracellular exosome / nucleoplasm / membrane / metal ion binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Gileadi, C. / Soundararajan, M. / Turnbull, A.P. / Elkins, J.M. / Papagrigoriou, E. / Pike, A.C.W. / Bunkoczi, G. / Gorrec, F. / Umeano, C. / von Delft, F. ...Gileadi, C. / Soundararajan, M. / Turnbull, A.P. / Elkins, J.M. / Papagrigoriou, E. / Pike, A.C.W. / Bunkoczi, G. / Gorrec, F. / Umeano, C. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C.H. / 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 | 2ode.cif.gz | 206.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ode.ent.gz | 160 KB | Display | PDB format |
PDBx/mmJSON format | 2ode.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/2ode ftp://data.pdbj.org/pub/pdb/validation_reports/od/2ode | HTTPS FTP |
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-Related structure data
Related structure data | 1zv4C 2a72C 2af0C 2bt2C 2bv1C 2es0C 2gtpC 2i59C 2ihbSC 2ihdC 2ik8C 2jm5C 2jnuC 2owiC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 5
NCS ensembles :
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 40162.578 Da / Num. of mol.: 2 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 #2: Protein | Mass: 16618.889 Da / Num. of mol.: 2 / Fragment: residues 42-180 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RGS8 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)R3 / References: UniProt: P57771 |
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-Non-polymers , 4 types, 661 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.20M NH4Cl, 20.0% PEG 6K, 10.0% EtGly, 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: 0.97901 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2006 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97901 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 80222 / Num. obs: 80222 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IHB Resolution: 1.9→29.4 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.958 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.13 / 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: 27.626 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→29.4 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.899→1.949 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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