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Yorodumi- PDB-5xf1: Structure of the Full-length glucagon class B G protein-coupled r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xf1 | |||||||||
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Title | Structure of the Full-length glucagon class B G protein-coupled receptor | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / Human GCGR receptor / Class B / 7TM domain / membrane / LCP / XFEL | |||||||||
Function / homology | Function and homology information regulation of glycogen metabolic process / glucagon receptor activity / cellular response to glucagon stimulus / response to starvation / exocytosis / peptide hormone binding / generation of precursor metabolites and energy / hormone-mediated signaling pathway / response to nutrient / viral release from host cell by cytolysis ...regulation of glycogen metabolic process / glucagon receptor activity / cellular response to glucagon stimulus / response to starvation / exocytosis / peptide hormone binding / generation of precursor metabolites and energy / hormone-mediated signaling pathway / response to nutrient / viral release from host cell by cytolysis / cellular response to starvation / peptidoglycan catabolic process / guanyl-nucleotide exchange factor activity / regulation of blood pressure / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon signaling in metabolic regulation / Glucagon-type ligand receptors / cell wall macromolecule catabolic process / glucose homeostasis / lysozyme / lysozyme activity / G alpha (s) signalling events / G alpha (q) signalling events / host cell cytoplasm / endosome / cell surface receptor signaling pathway / defense response to bacterium / positive regulation of gene expression / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Enterobacteria phage T4 (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å | |||||||||
Authors | Zhang, H. / Qiao, A. / Yang, D. / Yang, L. / Dai, A. / de Graaf, C. / Reedtz-Runge, S. / Dharmarajan, V. / Zhang, H. / Han, G.W. ...Zhang, H. / Qiao, A. / Yang, D. / Yang, L. / Dai, A. / de Graaf, C. / Reedtz-Runge, S. / Dharmarajan, V. / Zhang, H. / Han, G.W. / Grant, T. / Sierra, R. / Weierstall, U. / Nelson, G. / Liu, W. / Wu, Y. / Ma, L. / Cai, X. / Lin, G. / Wu, X. / Geng, Z. / Dong, Y. / Song, G. / Griffin, P. / Lau, J. / Cherezov, V. / Yang, H. / Hanson, M. / Stevens, R. / Jiang, H. / Wang, M. / Zhao, Q. / Wu, B. | |||||||||
Citation | Journal: Nature / Year: 2017 Title: Structure of the full-length glucagon class B G-protein-coupled receptor. Authors: Zhang, H. / Qiao, A. / Yang, D. / Yang, L. / Dai, A. / de Graaf, C. / Reedtz-Runge, S. / Dharmarajan, V. / Zhang, H. / Han, G.W. / Grant, T.D. / Sierra, R.G. / Weierstall, U. / Nelson, G. / ...Authors: Zhang, H. / Qiao, A. / Yang, D. / Yang, L. / Dai, A. / de Graaf, C. / Reedtz-Runge, S. / Dharmarajan, V. / Zhang, H. / Han, G.W. / Grant, T.D. / Sierra, R.G. / Weierstall, U. / Nelson, G. / Liu, W. / Wu, Y. / Ma, L. / Cai, X. / Lin, G. / Wu, X. / Geng, Z. / Dong, Y. / Song, G. / Griffin, P.R. / Lau, J. / Cherezov, V. / Yang, H. / Hanson, M.A. / Stevens, R.C. / Zhao, Q. / Jiang, H. / Wang, M.W. / Wu, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xf1.cif.gz | 726.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xf1.ent.gz | 603.5 KB | Display | PDB format |
PDBx/mmJSON format | 5xf1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/5xf1 ftp://data.pdbj.org/pub/pdb/validation_reports/xf/5xf1 | HTTPS FTP |
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-Related structure data
Related structure data | 5xezC 4l6rS C: citing same article (ref.) S: Starting model for refinement |
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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:
NCS ensembles :
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 65784.070 Da / Num. of mol.: 2 Fragment: UNP RESIDUES 27-256,UNP RESIDUES 2-161,UNP RESIDUES 260-432 Mutation: C54T, C97A Source method: isolated from a genetically manipulated source Details: The fusion protein of Glucagon receptor (UNP RESIDUES 27-256), Endolysin (UNP RESIDUES 2-161) and Glucagon receptor (UNP RESIDUES 260-432) 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 |
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-Antibody , 2 types, 4 molecules CHDL
#2: Antibody | Mass: 24977.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) #3: Antibody | Mass: 23263.811 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) |
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-Sugars , 3 types, 7 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose | #7: Sugar | ChemComp-NAG / | |
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-Non-polymers , 2 types, 3 molecules
#6: Chemical | #8: 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: 3.68 Å3/Da / Density % sol: 66.56 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 100mM HEPES, pH7.0, 200mM potassium phospphate monobasic, 20% PEG500DME, 10 mM gly-gly-glysine |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 20, 2016 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 3.19→50 Å / Num. obs: 49677 / % possible obs: 92.8 % / Redundancy: 2.8 % / Net I/σ(I): 3.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4L6R Resolution: 3.19→46.92 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.879 / SU B: 19.837 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R Free: 0.091 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 116.895 Å2
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Refinement step | Cycle: 1 / Resolution: 3.19→46.92 Å
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Refine LS restraints |
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