+Open data
-Basic information
Entry | Database: PDB / ID: 7ul2 | ||||||
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Title | CryoEM Structure of Inactive NTSR1 Bound to SR48692 and Nb6 | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Antagonist / Complex | ||||||
Function / homology | Function and homology information dynorphin receptor activity / response to acrylamide / regulation of saliva secretion / sensory perception of temperature stimulus / positive regulation of eating behavior / G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / adenylate cyclase-inhibiting opioid receptor signaling pathway / G protein-coupled opioid receptor activity / negative regulation of luteinizing hormone secretion ...dynorphin receptor activity / response to acrylamide / regulation of saliva secretion / sensory perception of temperature stimulus / positive regulation of eating behavior / G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / adenylate cyclase-inhibiting opioid receptor signaling pathway / G protein-coupled opioid receptor activity / negative regulation of luteinizing hormone secretion / symmetric synapse / G protein-coupled opioid receptor signaling pathway / D-aspartate import across plasma membrane / positive regulation of gamma-aminobutyric acid secretion / response to lipid / positive regulation of dopamine secretion / sensory perception / regulation of membrane depolarization / positive regulation of arachidonate secretion / positive regulation of potassium ion transmembrane transport / L-glutamate import across plasma membrane / conditioned place preference / regulation of respiratory gaseous exchange / positive regulation of inhibitory postsynaptic potential / maternal behavior / receptor serine/threonine kinase binding / neuropeptide binding / negative regulation of release of sequestered calcium ion into cytosol / negative regulation of systemic arterial blood pressure / positive regulation of glutamate secretion / positive regulation of p38MAPK cascade / positive regulation of inositol phosphate biosynthetic process / eating behavior / temperature homeostasis / detection of temperature stimulus involved in sensory perception of pain / behavioral response to cocaine / neuropeptide signaling pathway / estrous cycle / MECP2 regulates neuronal receptors and channels / axon terminus / sensory perception of pain / T-tubule / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Peptide ligand-binding receptors / adult locomotory behavior / positive regulation of release of sequestered calcium ion into cytosol / sarcoplasmic reticulum / learning / dendritic shaft / locomotory behavior / G protein-coupled receptor activity / cellular response to glucose stimulus / response to nicotine / response to insulin / terminal bouton / cytoplasmic side of plasma membrane / synaptic vesicle membrane / response to estrogen / presynaptic membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / G alpha (q) signalling events / cellular response to lipopolysaccharide / chemical synaptic transmission / postsynaptic membrane / perikaryon / response to ethanol / defense response to virus / dendritic spine / neuron projection / membrane raft / immune response / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / dendrite / positive regulation of gene expression / negative regulation of apoptotic process / protein-containing complex binding / cell surface / Golgi apparatus / endoplasmic reticulum / mitochondrion / nucleoplasm / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Lama glama (llama) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å | ||||||
Authors | Robertson, M.J. / Skiniotis, G. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: Structure determination of inactive-state GPCRs with a universal nanobody. Authors: Michael J Robertson / Makaía M Papasergi-Scott / Feng He / Alpay B Seven / Justin G Meyerowitz / Ouliana Panova / Maria Claudia Peroto / Tao Che / Georgios Skiniotis / Abstract: Cryogenic electron microscopy (cryo-EM) has widened the field of structure-based drug discovery by allowing for routine determination of membrane protein structures previously intractable. Despite ...Cryogenic electron microscopy (cryo-EM) has widened the field of structure-based drug discovery by allowing for routine determination of membrane protein structures previously intractable. Despite representing one of the largest classes of therapeutic targets, most inactive-state G protein-coupled receptors (GPCRs) have remained inaccessible for cryo-EM because their small size and membrane-embedded nature impedes projection alignment for high-resolution map reconstructions. Here we demonstrate that the same single-chain camelid antibody (nanobody) recognizing a grafted intracellular loop can be used to obtain cryo-EM structures of inactive-state GPCRs at resolutions comparable or better than those obtained by X-ray crystallography. Using this approach, we obtained structures of neurotensin 1 receptor bound to antagonist SR48692, μ-opioid receptor bound to alvimopan, apo somatostatin receptor 2 and histamine receptor 2 bound to famotidine. We expect this rapid, straightforward approach to facilitate the broad exploration of GPCR inactive states without the need for extensive engineering and crystallization. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ul2.cif.gz | 88.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ul2.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ul2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ul2_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7ul2_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7ul2_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 7ul2_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/7ul2 ftp://data.pdbj.org/pub/pdb/validation_reports/ul/7ul2 | HTTPS FTP |
-Related structure data
Related structure data | 26589MC 7ul3C 7ul4C 7ul5C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 47084.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NTSR1, NTRR, OPRK1, OPRK / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P30989, UniProt: P41145 |
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#2: Antibody | Mass: 14730.255 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) |
#3: Chemical | ChemComp-Q6Q / |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-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 / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 60.82 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 372987 / Symmetry type: POINT |