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Yorodumi- PDB-4hj0: Crystal structure of the human GIPr ECD in complex with Gipg013 F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hj0 | ||||||
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Title | Crystal structure of the human GIPr ECD in complex with Gipg013 Fab at 3-A resolution | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Glucagon receptor sub-family recognition fold | ||||||
Function / homology | Function and homology information gastric inhibitory peptide receptor activity / glucagon family peptide binding / gastric inhibitory peptide signaling pathway / desensitization of G protein-coupled receptor signaling pathway / positive regulation of cAMP-mediated signaling / endocrine pancreas development / response to fatty acid / G protein-coupled peptide receptor activity / peptide hormone binding / regulation of insulin secretion ...gastric inhibitory peptide receptor activity / glucagon family peptide binding / gastric inhibitory peptide signaling pathway / desensitization of G protein-coupled receptor signaling pathway / positive regulation of cAMP-mediated signaling / endocrine pancreas development / response to fatty acid / G protein-coupled peptide receptor activity / peptide hormone binding / regulation of insulin secretion / response to axon injury / response to glucose / activation of adenylate cyclase activity / response to nutrient / generation of precursor metabolites and energy / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / Glucagon-type ligand receptors / response to calcium ion / transmembrane signaling receptor activity / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / cell surface receptor signaling pathway / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Madhurantakam, C. / Ravn, P. / Gruetter, M.G. / Jackson, R.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structural and Pharmacological Characterization of Novel Potent and Selective Monoclonal Antibody Antagonists of Glucose-dependent Insulinotropic Polypeptide Receptor. Authors: Ravn, P. / Madhurantakam, C. / Kunze, S. / Matthews, E. / Priest, C. / O'Brien, S. / Collinson, A. / Papworth, M. / Fritsch-Fredin, M. / Jermutus, L. / Benthem, L. / Gruetter, M. / Jackson, R.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hj0.cif.gz | 199.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hj0.ent.gz | 158.8 KB | Display | PDB format |
PDBx/mmJSON format | 4hj0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hj0_validation.pdf.gz | 481.4 KB | Display | wwPDB validaton report |
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Full document | 4hj0_full_validation.pdf.gz | 549.6 KB | Display | |
Data in XML | 4hj0_validation.xml.gz | 46.2 KB | Display | |
Data in CIF | 4hj0_validation.cif.gz | 61.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/4hj0 ftp://data.pdbj.org/pub/pdb/validation_reports/hj/4hj0 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15764.310 Da / Num. of mol.: 2 / Fragment: Extra-cellular Domain, UNP residues 24-138 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GIPR / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / References: UniProt: P48546 #2: Protein | Mass: 23758.564 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEU / Cell line (production host): CHO / Production host: Homo sapiens (human) #3: Protein | Mass: 22691.947 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEU / Cell line (production host): CHO / Production host: Homo sapiens (human) |
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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: 2.24 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.02 M TAPS, 30% (w/v) PEG 10,000, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 29, 2010 |
Radiation | Monochromator: Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3→48.665 Å / Num. obs: 21995 / % possible obs: 100 % / Observed criterion σ(I): 2.6 |
Reflection shell | Resolution: 3→3.16 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QKH, 1GIG Resolution: 3→48.665 Å / SU ML: 1 / σ(F): 1.29 / Phase error: 31.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.75 Å2 / ksol: 0.306 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3→48.665 Å
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Refine LS restraints |
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LS refinement shell |
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