+Open data
-Basic information
Entry | Database: PDB / ID: 5vex | ||||||
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Title | Structure of the human GLP-1 receptor complex with NNC0640 | ||||||
Components | Glucagon-like peptide 1 receptor, Endolysin chimera | ||||||
Keywords | SIGNALING PROTEIN / GPCR / class B / 7TM domain / treatment of type 2 diabetes | ||||||
Function / homology | Function and homology information glucagon-like peptide 1 receptor activity / glucagon receptor activity / hormone secretion / positive regulation of blood pressure / post-translational protein targeting to membrane, translocation / regulation of heart contraction / response to psychosocial stress / peptide hormone binding / activation of adenylate cyclase activity / viral release from host cell by cytolysis ...glucagon-like peptide 1 receptor activity / glucagon receptor activity / hormone secretion / positive regulation of blood pressure / post-translational protein targeting to membrane, translocation / regulation of heart contraction / response to psychosocial stress / peptide hormone binding / activation of adenylate cyclase activity / viral release from host cell by cytolysis / negative regulation of blood pressure / cAMP-mediated signaling / peptidoglycan catabolic process / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon-type ligand receptors / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / transmembrane signaling receptor activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / host cell cytoplasm / learning or memory / cell surface receptor signaling pathway / defense response to bacterium / membrane / 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 | Song, G. / Yang, D. / Wang, Y. / Graaf, C.D. / Zhou, Q. / Jiang, S. / Liu, K. / Cai, X. / Dai, A. / Lin, G. ...Song, G. / Yang, D. / Wang, Y. / Graaf, C.D. / Zhou, Q. / Jiang, S. / Liu, K. / Cai, X. / Dai, A. / Lin, G. / Liu, D. / Wu, F. / Wu, Y. / Zhao, S. / Ye, L. / Han, G.W. / Lau, J. / Wu, B. / Hanson, M.A. / Liu, Z.-J. / Wang, M.-W. / Stevens, R.C. | ||||||
Citation | Journal: Nature / Year: 2017 Title: Human GLP-1 receptor transmembrane domain structure in complex with allosteric modulators. Authors: Song, G. / Yang, D. / Wang, Y. / de Graaf, C. / Zhou, Q. / Jiang, S. / Liu, K. / Cai, X. / Dai, A. / Lin, G. / Liu, D. / Wu, F. / Wu, Y. / Zhao, S. / Ye, L. / Han, G.W. / Lau, J. / Wu, B. / ...Authors: Song, G. / Yang, D. / Wang, Y. / de Graaf, C. / Zhou, Q. / Jiang, S. / Liu, K. / Cai, X. / Dai, A. / Lin, G. / Liu, D. / Wu, F. / Wu, Y. / Zhao, S. / Ye, L. / Han, G.W. / Lau, J. / Wu, B. / Hanson, M.A. / Liu, Z.J. / Wang, M.W. / Stevens, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vex.cif.gz | 355.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vex.ent.gz | 290.8 KB | Display | PDB format |
PDBx/mmJSON format | 5vex.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vex_validation.pdf.gz | 969.8 KB | Display | wwPDB validaton report |
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Full document | 5vex_full_validation.pdf.gz | 975.8 KB | Display | |
Data in XML | 5vex_validation.xml.gz | 30.4 KB | Display | |
Data in CIF | 5vex_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/5vex ftp://data.pdbj.org/pub/pdb/validation_reports/ve/5vex | HTTPS FTP |
-Related structure data
Related structure data | 5vewC 212lS 5ee7S 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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1 |
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2 |
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Unit cell |
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Details | THE AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN. |
-Components
#1: Protein | Mass: 52587.250 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus) Gene: GLP1R / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43220, UniProt: P00720, lysozyme #2: Chemical | Has protein modification | Y | |
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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: 3.32 Å3/Da / Density % sol: 62.92 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 0.4-0.45 M ammonium acetate, 0.1 M sodium acetate, pH 5.0-5.8, 38-40% PEG400 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 30, 2016 |
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: 24745 / % possible obs: 91.4 % / Redundancy: 2.9 % / Biso Wilson estimate: 92.82 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.6 / CC1/2: 0.66 / % possible all: 87.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 5ee7 and 212L Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.901 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.389
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Displacement parameters | Biso mean: 111.74 Å2
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Refine analyze | Luzzati coordinate error obs: 0.56 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.13 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
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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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