[English] 日本語
Yorodumi- PDB-5yqz: Structure of the glucagon receptor in complex with a glucagon analogue -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yqz | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the glucagon receptor in complex with a glucagon analogue | |||||||||
Components |
| |||||||||
Keywords | SIGNALING PROTEIN/HYDROLASE / Human GCGR receptor / Class B / 7TM domain / membrane / LCP / XFEL / SIGNALING PROTEIN / SIGNALING PROTEIN-HYDROLASE complex | |||||||||
Function / homology | Function and homology information glucagon receptor binding / regulation of glycogen metabolic process / glucagon receptor activity / negative regulation of execution phase of apoptosis / feeding behavior / : / response to starvation / cellular response to glucagon stimulus / positive regulation of calcium ion import / exocytosis ...glucagon receptor binding / regulation of glycogen metabolic process / glucagon receptor activity / negative regulation of execution phase of apoptosis / feeding behavior / : / response to starvation / cellular response to glucagon stimulus / positive regulation of calcium ion import / exocytosis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / peptide hormone binding / regulation of insulin secretion / Synthesis, secretion, and deacylation of Ghrelin / protein kinase A signaling / positive regulation of gluconeogenesis / viral release from host cell by cytolysis / cellular response to starvation / hormone-mediated signaling pathway / guanyl-nucleotide exchange factor activity / peptidoglycan catabolic process / response to nutrient / response to activity / positive regulation of peptidyl-threonine phosphorylation / generation of precursor metabolites and energy / gluconeogenesis / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Glucagon signaling in metabolic regulation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Glucagon-type ligand receptors / regulation of blood pressure / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cell wall macromolecule catabolic process / glucose homeostasis / lysozyme / positive regulation of peptidyl-serine phosphorylation / lysozyme activity / G alpha (s) signalling events / G alpha (q) signalling events / secretory granule lumen / host cell cytoplasm / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / endosome / defense response to bacterium / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / positive regulation of gene expression / negative regulation of apoptotic process / extracellular space / extracellular region / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Enterobacteria phage T4 (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Zhang, H. / Qiao, A. / Yang, L. / VAN EPS, N. / Frederiksen, K. / Yang, D. / Dai, A. / Cai, X. / Zhang, H. / Yi, C. ...Zhang, H. / Qiao, A. / Yang, L. / VAN EPS, N. / Frederiksen, K. / Yang, D. / Dai, A. / Cai, X. / Zhang, H. / Yi, C. / Can, C. / He, L. / Yang, H. / Lau, J. / Ernst, O. / Hanson, M. / Stevens, R. / Wang, M. / Seedtz-Runge, S. / Jiang, H. / Zhao, Q. / Wu, B. | |||||||||
Funding support | China, 2items
| |||||||||
Citation | Journal: Nature / Year: 2018 Title: Structure of the glucagon receptor in complex with a glucagon analogue. Authors: Zhang, H. / Qiao, A. / Yang, L. / Van Eps, N. / Frederiksen, K.S. / Yang, D. / Dai, A. / Cai, X. / Zhang, H. / Yi, C. / Cao, C. / He, L. / Yang, H. / Lau, J. / Ernst, O.P. / Hanson, M.A. / ...Authors: Zhang, H. / Qiao, A. / Yang, L. / Van Eps, N. / Frederiksen, K.S. / Yang, D. / Dai, A. / Cai, X. / Zhang, H. / Yi, C. / Cao, C. / He, L. / Yang, H. / Lau, J. / Ernst, O.P. / Hanson, M.A. / Stevens, R.C. / Wang, M.W. / Reedtz-Runge, S. / Jiang, H. / Zhao, Q. / Wu, B. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5yqz.cif.gz | 136.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5yqz.ent.gz | 101.7 KB | Display | PDB format |
PDBx/mmJSON format | 5yqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/5yqz ftp://data.pdbj.org/pub/pdb/validation_reports/yq/5yqz | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 65799.062 Da / Num. of mol.: 1 / Mutation: R173A,C1053A, C1096Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus) Gene: GCGR, e, T4Tp126 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P47871, UniProt: D9IEF7, lysozyme | ||||
---|---|---|---|---|---|
#2: Protein/peptide | Mass: 3345.674 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01275*PLUS | ||||
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-OLC / ( #5: Chemical | ChemComp-PO4 / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.1 Å3/Da / Density % sol: 75.87 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 8 Details: 100 mM Tris, pH 8.0, 70-120 mM potassium phosphate dibasic, 27-33% (v/v) PEG 200 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 28879 / % possible obs: 97.8 % / Redundancy: 10.1 % / Biso Wilson estimate: 112.9 Å2 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 3→3.11 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XEZ, 4LF3, 2RH1 Resolution: 3→48.59 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.846 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.541 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.524 / SU Rfree Blow DPI: 0.327 / SU Rfree Cruickshank DPI: 0.335
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 129.8 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.53 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3→48.59 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.11 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
|