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Yorodumi- PDB-5otw: Extracellular domain of GLP-1 receptor in complex with GLP-1 vari... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5otw | ||||||
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Title | Extracellular domain of GLP-1 receptor in complex with GLP-1 variant Ala8Hcs/Thr11Cys | ||||||
Components |
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Keywords | SIGNALING PROTEIN / glucagon-like peptide 1 / GPCR / cyclic peptides | ||||||
Function / homology | Function and homology information glucagon receptor binding / glucagon-like peptide 1 receptor activity / glucagon receptor activity / hormone secretion / positive regulation of blood pressure / negative regulation of execution phase of apoptosis / post-translational protein targeting to membrane, translocation / feeding behavior / response to psychosocial stress / regulation of heart contraction ...glucagon receptor binding / glucagon-like peptide 1 receptor activity / glucagon receptor activity / hormone secretion / positive regulation of blood pressure / negative regulation of execution phase of apoptosis / post-translational protein targeting to membrane, translocation / feeding behavior / response to psychosocial stress / regulation of heart contraction / positive regulation of calcium ion import / cellular response to glucagon stimulus / 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 / activation of adenylate cyclase activity / positive regulation of gluconeogenesis / protein kinase A signaling / negative regulation of blood pressure / cAMP-mediated signaling / positive regulation of peptidyl-threonine phosphorylation / response to activity / gluconeogenesis / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / transmembrane signaling receptor activity / Glucagon signaling in metabolic regulation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Glucagon-type ligand receptors / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / positive regulation of peptidyl-serine phosphorylation / glucose homeostasis / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / G alpha (q) signalling events / secretory granule lumen / positive regulation of ERK1 and ERK2 cascade / learning or memory / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / negative regulation of apoptotic process / extracellular space / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Mortensen, S. | ||||||
Citation | Journal: Biochemistry / Year: 2018 Title: alpha-Helix or beta-Turn? An Investigation into N-Terminally Constrained Analogues of Glucagon-like Peptide 1 (GLP-1) and Exendin-4. Authors: Oddo, A. / Mortensen, S. / Thogersen, H. / De Maria, L. / Hennen, S. / McGuire, J.N. / Kofoed, J. / Linderoth, L. / Reedtz-Runge, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5otw.cif.gz | 120.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5otw.ent.gz | 93.6 KB | Display | PDB format |
PDBx/mmJSON format | 5otw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5otw_validation.pdf.gz | 444.9 KB | Display | wwPDB validaton report |
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Full document | 5otw_full_validation.pdf.gz | 445.5 KB | Display | |
Data in XML | 5otw_validation.xml.gz | 13 KB | Display | |
Data in CIF | 5otw_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/5otw ftp://data.pdbj.org/pub/pdb/validation_reports/ot/5otw | HTTPS FTP |
-Related structure data
Related structure data | 5ottC 5otuC 5otvC 5otxC 4zgmS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13547.892 Da / Num. of mol.: 2 / Fragment: extracellular domain, UNP residues 24-139 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GLP1R / Production host: Escherichia coli (E. coli) / References: UniProt: P43220 #2: Protein/peptide | Mass: 3407.830 Da / Num. of mol.: 2 / Mutation: A8HCS, T11C / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01275 #3: 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: 1.99 Å3/Da / Density % sol: 38.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Morpheus from Molecular Dimensions, solution E12: 0.12 M ethylene Glycols, 0.1 M Buffer system 3 pH 8.5, 12.5% (v/v) MPD, 12.5% (w/v) PEG1000, 12.5% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54187 Å |
Detector | Type: DECTRIS PILATUS3 R 1M / Detector: PIXEL / Date: Feb 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→42.26 Å / Num. obs: 15304 / % possible obs: 98.5 % / Redundancy: 5.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.049 / Rsym value: 0.118 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 5.53 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.9 / Num. measured obs: 4245 / Num. unique all: 767 / CC1/2: 0.742 / Rpim(I) all: 0.459 / Rrim(I) all: 1.086 / % possible all: 95.64 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZGM Resolution: 2.1→42.252 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.54
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→42.252 Å
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Refine LS restraints |
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LS refinement shell |
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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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