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- PDB-8qot: Structure of the mu opioid receptor bound to the antagonist nanob... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qot | ||||||||||||
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Title | Structure of the mu opioid receptor bound to the antagonist nanobody NbE | ||||||||||||
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![]() | MEMBRANE PROTEIN / opioid receptor / nanobody / antagonist / NabFab / MOR | ||||||||||||
Function / homology | ![]() Opioid Signalling / spine apparatus / beta-endorphin receptor activity / morphine receptor activity / negative regulation of Wnt protein secretion / Peptide ligand-binding receptors / adenylate cyclase-inhibiting opioid receptor signaling pathway / positive regulation of appetite / G-protein activation / G protein-coupled opioid receptor activity ...Opioid Signalling / spine apparatus / beta-endorphin receptor activity / morphine receptor activity / negative regulation of Wnt protein secretion / Peptide ligand-binding receptors / adenylate cyclase-inhibiting opioid receptor signaling pathway / positive regulation of appetite / G-protein activation / G protein-coupled opioid receptor activity / negative regulation of luteinizing hormone secretion / G protein-coupled opioid receptor signaling pathway / sperm ejaculation / G alpha (i) signalling events / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / negative regulation of nitric oxide biosynthetic process / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / neuropeptide binding / negative regulation of cAMP-mediated signaling / regulation of NMDA receptor activity / positive regulation of neurogenesis / eating behavior / negative regulation of cytosolic calcium ion concentration / transmission of nerve impulse / social behavior / G-protein alpha-subunit binding / GABA-ergic synapse / voltage-gated calcium channel activity / neuropeptide signaling pathway / positive regulation of gluconeogenesis / sensory perception of pain / dendrite membrane / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / presynaptic modulation of chemical synaptic transmission / excitatory postsynaptic potential / dendrite cytoplasm / locomotory behavior / G protein-coupled receptor activity / adenylate cyclase-activating dopamine receptor signaling pathway / G-protein beta-subunit binding / phospholipase C-activating G protein-coupled receptor signaling pathway / presynaptic membrane / postsynaptic membrane / perikaryon / response to ethanol / positive regulation of ERK1 and ERK2 cascade / endosome / neuron projection / G protein-coupled receptor signaling pathway / protein domain specific binding / axon / focal adhesion / dendrite / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() synthetic construct (others) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
![]() | Yu, J. / Kumar, A. / Zhang, X. / Martin, C. / Raia, P. / Manglik, A. / Ballet, S. / Boland, A. / Stoeber, M. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis of μ-Opioid Receptor-Targeting by a Nanobody Antagonist. Authors: Jun Yu / Amit Kumar / Xuefeng Zhang / Charlotte Martin / Pierre Raia / Antoine Koehl / Toon Laeremans / Jan Steyaert / Aashish Manglik / Steven Ballet / Andreas Boland / Miriam Stoeber / ![]() ![]() ![]() Abstract: The μ-opioid receptor (μOR), a prototypical member of the G protein-coupled receptor (GPCR) family, is the molecular target of opioid analgesics such as morphine and fentanyl. Due to the ...The μ-opioid receptor (μOR), a prototypical member of the G protein-coupled receptor (GPCR) family, is the molecular target of opioid analgesics such as morphine and fentanyl. Due to the limitations and severe side effects of currently available opioid drugs, there is considerable interest in developing novel modulators of μOR function. Most GPCR ligands today are small molecules, however biologics, including antibodies and nanobodies, are emerging as alternative therapeutics with clear advantages such as affinity and target selectivity. Here, we describe the nanobody NbE, which selectively binds to the μOR and acts as an antagonist. We functionally characterize NbE as an extracellular and genetically encoded μOR ligand and uncover the molecular basis for μOR antagonism by solving the cryo-EM structure of the NbE-μOR complex. NbE displays a unique ligand binding mode and achieves μOR selectivity by interactions with the orthosteric pocket and extracellular receptor loops. Based on a β-hairpin loop formed by NbE that deeply inserts into the μOR and centers most binding contacts, we design short peptide analogues that retain μOR antagonism. The work illustrates the potential of nanobodies to uniquely engage with GPCRs and describes novel μOR ligands that can serve as a basis for therapeutic developments. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189.1 KB | Display | ![]() |
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PDB format | ![]() | 140.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 38.4 KB | Display | |
Data in CIF | ![]() | 55.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 18541MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 53994.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: MOR-2xSTREP-8xHIS / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 18458.662 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: synthesized nanobody NbE-6xHis / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Antibody | Mass: 28220.525 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Signal sequence-NabFab HC / Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
#4: Antibody | Mass: 25794.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
#5: Antibody | Mass: 17414.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Signal sequence-6xHis Anti-Fab nanobody / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: MOR-NbE-NabFab-AntiFab complex / Type: COMPLEX Details: Mu-opioid receptor bound to a nanobody antagonist (NbE), and NabFab module used as fiducial marker. Entity ID: all / Source: MULTIPLE SOURCES | |||||||||||||||||||||||||
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Molecular weight | Value: 0.12 MDa | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | |||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: MOR receptor was expressed and purified in insect cells in isolation. NbE was expressed and purified in E. coli. NabFab module was expressed and purified in E. coli. All purified components ...Details: MOR receptor was expressed and purified in insect cells in isolation. NbE was expressed and purified in E. coli. NabFab module was expressed and purified in E. coli. All purified components were incubated and formed readily a stable complex. Final complex was purified over size exclusion chromatography. | |||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 288 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 95 K / Temperature (min): 90 K |
Image recording | Average exposure time: 52 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 5938 |
Image scans | Width: 4096 / Height: 4096 |
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Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 6063911 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 445766 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 68 / Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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Refinement | Cross valid method: NONE |