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Yorodumi- PDB-6b3j: 3.3 angstrom phase-plate cryo-EM structure of a biased agonist-bo... -
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-Basic information
Entry | Database: PDB / ID: 6b3j | |||||||||||||||
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Title | 3.3 angstrom phase-plate cryo-EM structure of a biased agonist-bound human GLP-1 receptor-Gs complex | |||||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / class B G protein-coupled receptor / agonist-receptor-G protein ternary complex / glucagon-like peptide 1 receptor / active-state G protein-coupled receptor / phase plate / phase contrast / single particle cryo-em | |||||||||||||||
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 / activation of adenylate cyclase activity / response to psychosocial stress / peptide hormone binding / cAMP-mediated signaling ...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 / activation of adenylate cyclase activity / response to psychosocial stress / peptide hormone binding / cAMP-mediated signaling / negative regulation of blood pressure / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Activation of the phototransduction cascade / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Glucagon signaling in metabolic regulation / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G beta:gamma signalling through CDC42 / Vasopressin regulates renal water homeostasis via Aquaporins / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Glucagon-type ligand receptors / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / G alpha (z) signalling events / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / cellular response to catecholamine stimulus / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / GPER1 signaling / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / cellular response to prostaglandin E stimulus / transmembrane signaling receptor activity / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / learning or memory / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / protein-containing complex binding / signal transduction / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) Lama glama (llama) synthetic construct (others) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||
Authors | Liang, Y.L. / Khoshouei, M. / Glukhova, A. / Furness, S.G.B. / Koole, C. / Zhao, P. / Clydesdale, L. / Thal, D.M. / Radjainia, M. / Danev, R. ...Liang, Y.L. / Khoshouei, M. / Glukhova, A. / Furness, S.G.B. / Koole, C. / Zhao, P. / Clydesdale, L. / Thal, D.M. / Radjainia, M. / Danev, R. / Baumeister, W. / Wang, M.W. / Miller, L.J. / Christopoulos, A. / Sexton, P.M. / Wootten, D. | |||||||||||||||
Funding support | Australia, 4items
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Citation | Journal: Nature / Year: 2018 Title: Phase-plate cryo-EM structure of a biased agonist-bound human GLP-1 receptor-Gs complex. Authors: Yi-Lynn Liang / Maryam Khoshouei / Alisa Glukhova / Sebastian G B Furness / Peishen Zhao / Lachlan Clydesdale / Cassandra Koole / Tin T Truong / David M Thal / Saifei Lei / Mazdak Radjainia ...Authors: Yi-Lynn Liang / Maryam Khoshouei / Alisa Glukhova / Sebastian G B Furness / Peishen Zhao / Lachlan Clydesdale / Cassandra Koole / Tin T Truong / David M Thal / Saifei Lei / Mazdak Radjainia / Radostin Danev / Wolfgang Baumeister / Ming-Wei Wang / Laurence J Miller / Arthur Christopoulos / Patrick M Sexton / Denise Wootten / Abstract: The class B glucagon-like peptide-1 (GLP-1) G protein-coupled receptor is a major target for the treatment of type 2 diabetes and obesity. Endogenous and mimetic GLP-1 peptides exhibit biased agonism- ...The class B glucagon-like peptide-1 (GLP-1) G protein-coupled receptor is a major target for the treatment of type 2 diabetes and obesity. Endogenous and mimetic GLP-1 peptides exhibit biased agonism-a difference in functional selectivity-that may provide improved therapeutic outcomes. Here we describe the structure of the human GLP-1 receptor in complex with the G protein-biased peptide exendin-P5 and a Gα heterotrimer, determined at a global resolution of 3.3 Å. At the extracellular surface, the organization of extracellular loop 3 and proximal transmembrane segments differs between our exendin-P5-bound structure and previous GLP-1-bound GLP-1 receptor structure. At the intracellular face, there was a six-degree difference in the angle of the Gαs-α5 helix engagement between structures, which was propagated across the G protein heterotrimer. In addition, the structures differed in the rate and extent of conformational reorganization of the Gα protein. Our structure provides insights into the molecular basis of biased agonism. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6b3j.cif.gz | 217.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b3j.ent.gz | 171.9 KB | Display | PDB format |
PDBx/mmJSON format | 6b3j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6b3j_validation.pdf.gz | 923.9 KB | Display | wwPDB validaton report |
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Full document | 6b3j_full_validation.pdf.gz | 929.6 KB | Display | |
Data in XML | 6b3j_validation.xml.gz | 40.7 KB | Display | |
Data in CIF | 6b3j_validation.cif.gz | 63.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/6b3j ftp://data.pdbj.org/pub/pdb/validation_reports/b3/6b3j | HTTPS FTP |
-Related structure data
Related structure data | 7039MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
-Guanine nucleotide-binding protein ... , 3 types, 3 molecules ABG
#3: Protein | Mass: 45683.434 Da / Num. of mol.: 1 Mutation: S54N, G226A, E268A, N271K, N274D, R280K, T284D, I285T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNAS, GNAS1, GSP / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P63092 |
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#4: Protein | Mass: 38534.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P62873 |
#5: Protein | Mass: 7861.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P59768 |
-Protein / Protein/peptide / Antibody , 3 types, 3 molecules RPN
#1: Protein | Mass: 56748.418 Da / Num. of mol.: 1 / Fragment: residues 24-463 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GLP1R / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P43220 |
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#2: Protein/peptide | Mass: 4228.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#6: Antibody | Mass: 15140.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex of a full-length, active-state glucagon-like peptide-1 receptor with exendin-P5 ligand, heterotrimeric Gs protein and nanobody 35. Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.15 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 47170 X / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 8 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2793 |
EM imaging optics | Energyfilter name: Gatan Quantum energy filter / Phase plate: The images were taken at 500 defocus |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 50 |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | |||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Details: Phase plate CTF correction / Type: NONE | |||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 614883 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||
Atomic model building | Details: 3C5T was rigid body fitted with minimal manual adjustments. The rest of the chain R and chains A,B,G,N were extensively remodeled. Chain P was built de novo. | |||||||||||||||||||||||||||||||||||
Atomic model building |
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Refine LS restraints |
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