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Yorodumi- PDB-1y3a: Structure of G-Alpha-I1 bound to a GDP-selective peptide provides... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y3a | ||||||
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Title | Structure of G-Alpha-I1 bound to a GDP-selective peptide provides insight into guanine nucleotide exchange | ||||||
Components |
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Keywords | SIGNALING PROTEIN / PROTEIN-PEPTIDE COMPLEX | ||||||
Function / homology | Function and homology information Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / cell cortex region / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cellular response to forskolin / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Regulation of insulin secretion ...Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / cell cortex region / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cellular response to forskolin / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Regulation of insulin secretion / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / ADP signalling through P2Y purinoceptor 12 / response to peptide hormone / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (z) signalling events / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / GDP binding / heterotrimeric G-protein complex / cell cortex / G alpha (i) signalling events / midbody / G alpha (s) signalling events / Extra-nuclear estrogen signaling / cell cycle / G protein-coupled receptor signaling pathway / lysosomal membrane / cell division / GTPase activity / centrosome / GTP binding / nucleolus / magnesium ion binding / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Johnston, C.A. / Willard, F.S. / Jezyk, M.R. / Fredericks, Z. / Bodor, E.T. / Jones, M.B. / Blaesius, R. / Harden, T.K. / Sondek, J. / Watts, V.J. ...Johnston, C.A. / Willard, F.S. / Jezyk, M.R. / Fredericks, Z. / Bodor, E.T. / Jones, M.B. / Blaesius, R. / Harden, T.K. / Sondek, J. / Watts, V.J. / Ramer, J.K. / Siderovski, D.P. | ||||||
Citation | Journal: Structure / Year: 2005 Title: Structure of G-Alpha-I1 bound to a GDP-selective peptide provides insight into guanine nucleotide exchange Authors: Johnston, C.A. / Willard, F.S. / Jezyk, M.R. / Fredericks, Z. / Bodor, E.T. / Jones, M.B. / Blaesius, R. / Watts, V.J. / Harden, T.K. / Sondek, J. / Ramer, J.K. / Siderovski, D.P. | ||||||
History |
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Remark 999 | SEQUENCE THERE IS NO SUITABLE SEQUENCE DATABASE REFERENCE FOR CHAINS E-H AT THE TIME OF PROCESSING. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y3a.cif.gz | 264.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y3a.ent.gz | 213.4 KB | Display | PDB format |
PDBx/mmJSON format | 1y3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y3/1y3a ftp://data.pdbj.org/pub/pdb/validation_reports/y3/1y3a | HTTPS FTP |
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-Related structure data
Related structure data | 1bofS 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 37603.809 Da / Num. of mol.: 4 / Fragment: sequence database residues 25-353 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1 / Plasmid: pPRO-EXHTb / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63096 #2: Protein/peptide | Mass: 2037.277 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: PROTEIN SELECTED BY PHAGE DISPLAY / Plasmid: pPRO-EXHTb / Production host: Escherichia coli (E. coli) #3: Chemical | ChemComp-GDP / #4: 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: 2.995 Å3/Da / Density % sol: 57.35 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 8000, sucrose, sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0093144 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 3, 2004 |
Radiation | Monochromator: APS BEAMLINE 22-ID (SER-CAT) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0093144 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 61384 / % possible obs: 78.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.7 % / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BOF Resolution: 2.5→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.53 Å / Rfactor Rfree error: 0.017
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Xplor file |
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