+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-44635 | |||||||||
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Title | Inactive mu opioid receptor bound to Nb6, naloxone and NAM | |||||||||
Map data | sharpened density file for MORk/Nb6 bound to naloxone and 368 | |||||||||
Sample |
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Keywords | G-protein coupled receptor / inactive / opioid / allosteric modulator / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information 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 cAMP-mediated signaling / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / neuropeptide binding / regulation of NMDA receptor activity / positive regulation of neurogenesis / eating behavior / negative regulation of cytosolic calcium ion concentration / transmission of nerve impulse / social behavior / neuropeptide signaling pathway / G-protein alpha-subunit binding / voltage-gated calcium channel activity / GABA-ergic synapse / positive regulation of gluconeogenesis / dendrite membrane / sensory perception of pain / presynaptic modulation of chemical synaptic transmission / dendrite cytoplasm / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / excitatory postsynaptic potential / locomotory behavior / G protein-coupled receptor activity / adenylate cyclase-activating dopamine receptor signaling pathway / G-protein beta-subunit binding / presynaptic membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / perikaryon / postsynaptic membrane / 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 | Mus musculus (house mouse) / Lama glama (llama) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.26 Å | |||||||||
Authors | O'Brien ES / Wang H / Kaavya Krishna K / Zhang C / Kobilka BK | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2024 Title: A µ-opioid receptor modulator that works cooperatively with naloxone. Authors: Evan S O'Brien / Vipin Ashok Rangari / Amal El Daibani / Shainnel O Eans / Haylee R Hammond / Elizabeth White / Haoqing Wang / Yuki Shiimura / Kaavya Krishna Kumar / Qianru Jiang / Kevin ...Authors: Evan S O'Brien / Vipin Ashok Rangari / Amal El Daibani / Shainnel O Eans / Haylee R Hammond / Elizabeth White / Haoqing Wang / Yuki Shiimura / Kaavya Krishna Kumar / Qianru Jiang / Kevin Appourchaux / Weijiao Huang / Chensong Zhang / Brandon J Kennedy / Jesper M Mathiesen / Tao Che / Jay P McLaughlin / Susruta Majumdar / Brian K Kobilka / Abstract: The µ-opioid receptor (µOR) is a well-established target for analgesia, yet conventional opioid receptor agonists cause serious adverse effects, notably addiction and respiratory depression. These ...The µ-opioid receptor (µOR) is a well-established target for analgesia, yet conventional opioid receptor agonists cause serious adverse effects, notably addiction and respiratory depression. These factors have contributed to the current opioid overdose epidemic driven by fentanyl, a highly potent synthetic opioid. µOR negative allosteric modulators (NAMs) may serve as useful tools in preventing opioid overdose deaths, but promising chemical scaffolds remain elusive. Here we screened a large DNA-encoded chemical library against inactive µOR, counter-screening with active, G-protein and agonist-bound receptor to 'steer' hits towards conformationally selective modulators. We discovered a NAM compound with high and selective enrichment to inactive µOR that enhances the affinity of the key opioid overdose reversal molecule, naloxone. The NAM works cooperatively with naloxone to potently block opioid agonist signalling. Using cryogenic electron microscopy, we demonstrate that the NAM accomplishes this effect by binding a site on the extracellular vestibule in direct contact with naloxone while stabilizing a distinct inactive conformation of the extracellular portions of the second and seventh transmembrane helices. The NAM alters orthosteric ligand kinetics in therapeutically desirable ways and works cooperatively with low doses of naloxone to effectively inhibit various morphine-induced and fentanyl-induced behavioural effects in vivo while minimizing withdrawal behaviours. Our results provide detailed structural insights into the mechanism of negative allosteric modulation of the µOR and demonstrate how this can be exploited in vivo. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_44635.map.gz | 96.9 MB | EMDB map data format | |
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Header (meta data) | emd-44635-v30.xml emd-44635.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
Images | emd_44635.png | 64.2 KB | ||
Filedesc metadata | emd-44635.cif.gz | 6.1 KB | ||
Others | emd_44635_half_map_1.map.gz emd_44635_half_map_2.map.gz | 95.6 MB 95.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44635 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44635 | HTTPS FTP |
-Validation report
Summary document | emd_44635_validation.pdf.gz | 850.8 KB | Display | EMDB validaton report |
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Full document | emd_44635_full_validation.pdf.gz | 850.3 KB | Display | |
Data in XML | emd_44635_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | emd_44635_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44635 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44635 | HTTPS FTP |
-Related structure data
Related structure data | 9bjkMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_44635.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | sharpened density file for MORk/Nb6 bound to naloxone and 368 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.741 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map B for MORk/Nb6 bound to naloxone and 368
File | emd_44635_half_map_1.map | ||||||||||||
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Annotation | half map B for MORk/Nb6 bound to naloxone and 368 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A for MORk/Nb6 bound to naloxone and 368
File | emd_44635_half_map_2.map | ||||||||||||
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Annotation | half map A for MORk/Nb6 bound to naloxone and 368 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : mu-type opioid receptor with kappa-type opioid receptor ICL3 in c...
Entire | Name: mu-type opioid receptor with kappa-type opioid receptor ICL3 in complex with Nb6, naloxone and a negative allosteric modulator |
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Components |
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-Supramolecule #1: mu-type opioid receptor with kappa-type opioid receptor ICL3 in c...
Supramolecule | Name: mu-type opioid receptor with kappa-type opioid receptor ICL3 in complex with Nb6, naloxone and a negative allosteric modulator type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: kappa opioid receptor Nanobody 6
Macromolecule | Name: kappa opioid receptor Nanobody 6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Lama glama (llama) |
Molecular weight | Theoretical: 14.730255 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAQVQLQESG GGLVQAGESL RLSCAASGTI FRLYDMGWYR RVSGNQRELV ASITSGGSTK YGDSVKGRFT ISRDNAKNTV YLQMSSLKP EDTAVYYCNA EYRTGIWEEL LDGWGQGTQV TVSSHHHHHH EPEA |
-Macromolecule #2: Mu-type opioid receptor
Macromolecule | Name: Mu-type opioid receptor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 47.920734 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MKTIIALSYI FCLVFADYKD DDDAMGPGNI SDCSDPLAPA SCSPAPGSWL NLSHVDGNQS DPCGPNRTGL GGSHSLCPQT GSPSMVTAI TIMALYSIVC VVGLFGNFLV MYVIVRYTKM KTATNIYIFN LALADALATS TLPFQSVNYL MGTWPFGNIL C KIVISIDY ...String: MKTIIALSYI FCLVFADYKD DDDAMGPGNI SDCSDPLAPA SCSPAPGSWL NLSHVDGNQS DPCGPNRTGL GGSHSLCPQT GSPSMVTAI TIMALYSIVC VVGLFGNFLV MYVIVRYTKM KTATNIYIFN LALADALATS TLPFQSVNYL MGTWPFGNIL C KIVISIDY YNMFTSIFTL CTMSVDRYIA VCHPVKALDF RTPRNAKIVN VCNWILSSAI GLPVMFMATT KYRQGSIDCT LT FSHPTWY WENLLKICVF IFAFIMPVLI ITVCYGLMIL RLKSVRLLSG SREKDRNLRR ITRMVLVVVA VFIVCWTPIH IYV IIKALI TIPETTFQTV SWHFCIALGY TNSCLNPVLY AFLDENFKRC FREFCIPTSS TIEQQNSARI RQNTREHPST ANTV DRTNH QLENLEAETA PLPDIHHHHH H UniProtKB: Mu-type opioid receptor |
-Macromolecule #3: Naloxone
Macromolecule | Name: Naloxone / type: ligand / ID: 3 / Number of copies: 1 / Formula: A1APV |
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Molecular weight | Theoretical: 327.374 Da |
-Macromolecule #4: Nalpha-[({(1M)-1-[5-(benzyloxy)pyridin-3-yl]naphthalen-2-yl}sulfa...
Macromolecule | Name: Nalpha-[({(1M)-1-[5-(benzyloxy)pyridin-3-yl]naphthalen-2-yl}sulfanyl)acetyl]-3-methoxy-N,4-dimethyl-L-phenylalaninamide type: ligand / ID: 4 / Number of copies: 1 / Formula: A1APU |
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Molecular weight | Theoretical: 605.746 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 128613 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |