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Yorodumi- PDB-6ln2: Crystal structure of full length human GLP1 receptor in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ln2 | ||||||
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Title | Crystal structure of full length human GLP1 receptor in complex with Fab fragment (Fab7F38) | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Full length Human GLP1 receptor / Class B / Fab7F38 / TMD / NAM PF06372222 / LCP | ||||||
Function / homology | Function and homology information glucagon-like peptide 1 receptor activity / alkane catabolic process / glucagon receptor activity / hormone secretion / positive regulation of blood pressure / post-translational protein targeting to membrane, translocation / response to psychosocial stress / regulation of heart contraction / peptide hormone binding / activation of adenylate cyclase activity ...glucagon-like peptide 1 receptor activity / alkane catabolic process / glucagon receptor activity / hormone secretion / positive regulation of blood pressure / post-translational protein targeting to membrane, translocation / response to psychosocial stress / regulation of heart contraction / peptide hormone binding / activation of adenylate cyclase activity / negative regulation of blood pressure / cAMP-mediated signaling / adenylate cyclase-activating G protein-coupled receptor signaling pathway / transmembrane signaling receptor activity / Glucagon-type ligand receptors / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / learning or memory / cell surface receptor signaling pathway / electron transfer activity / iron ion binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Clostridium pasteurianum (bacteria) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Wu, F. / Yang, L. / Hang, K. / Laursen, M. / Wu, L. / Han, G.W. / Ren, Q. / Roed, N.K. / Lin, G. / Hanson, M. ...Wu, F. / Yang, L. / Hang, K. / Laursen, M. / Wu, L. / Han, G.W. / Ren, Q. / Roed, N.K. / Lin, G. / Hanson, M. / Jiang, H. / Wang, M. / Reedtz-Runge, S. / Song, G. / Stevens, R.C. | ||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Full-length human GLP-1 receptor structure without orthosteric ligands. Authors: Wu, F. / Yang, L. / Hang, K. / Laursen, M. / Wu, L. / Han, G.W. / Ren, Q. / Roed, N.K. / Lin, G. / Hanson, M.A. / Jiang, H. / Wang, M.W. / Reedtz-Runge, S. / Song, G. / 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 | 6ln2.cif.gz | 351.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ln2.ent.gz | 282.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ln2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ln2_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6ln2_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6ln2_validation.xml.gz | 31.6 KB | Display | |
Data in CIF | 6ln2_validation.cif.gz | 43.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/6ln2 ftp://data.pdbj.org/pub/pdb/validation_reports/ln/6ln2 | HTTPS FTP |
-Related structure data
Related structure data | 5nx2S 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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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN. |
-Components
-Antibody , 2 types, 2 molecules BC
#2: Antibody | Mass: 23307.939 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) |
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#3: Antibody | Mass: 24476.268 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) |
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 54619.996 Da / Num. of mol.: 1 Mutation: S193C,I196F,S225A,M233C,S271A,I317C,G318I,K346A,C347F,G361C,E387D Source method: isolated from a genetically manipulated source Details: The fusion protein of GLP1 receptor (UNP residues 24-260), Rubredoxin (UNP residues 1-54) and GLP1 receptor (UNP residues 262-439) Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Clostridium pasteurianum (bacteria) Gene: GLP1R / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43220, UniProt: P00268 |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 2 molecules
#5: Chemical | ChemComp-ZN / |
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#6: Chemical | ChemComp-97Y / |
-Details
Has ligand of interest | 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: 3.21 Å3/Da / Density % sol: 61.66 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 200-300 mM Ammonium formate, 36% PEG 400, 5%-10% (w/v) Guanidine hydrochloride PH range: pH 6.2-6.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→45.7 Å / Num. obs: 22019 / % possible obs: 97.8 % / Redundancy: 4.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 3.2→3.37 Å / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3109 / CC1/2: 0.526 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NX2 Resolution: 3.2→30 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.886 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.453
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Displacement parameters | Biso max: 261 Å2 / Biso mean: 136.81 Å2 / Biso min: 58.31 Å2
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Refine analyze | Luzzati coordinate error obs: 0 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
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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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