+Open data
-Basic information
Entry | Database: PDB / ID: 6u1n | |||||||||
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Title | GPCR-Beta arrestin structure in lipid bilayer | |||||||||
Components |
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Keywords | SIGNALING PROTEIN/IMMUNE SYSTEM / Arrestin / GPCR / complex / signaling / SIGNALING PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / sensory perception of touch / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / G alpha (s) signalling events / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity ...V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / sensory perception of touch / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / G alpha (s) signalling events / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / alpha-1B adrenergic receptor binding / follicle-stimulating hormone signaling pathway / protein phosphorylated amino acid binding / angiotensin receptor binding / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / Muscarinic acetylcholine receptors / symmetric synapse / Golgi Associated Vesicle Biogenesis / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / MAP2K and MAPK activation / Ub-specific processing proteases / G protein-coupled acetylcholine receptor activity / hemostasis / positive regulation of systemic arterial blood pressure / cholinergic synapse / telencephalon development / positive regulation of smooth muscle cell apoptotic process / regulation of smooth muscle contraction / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / negative regulation of interleukin-8 production / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / regulation of G protein-coupled receptor signaling pathway / G protein-coupled serotonin receptor activity / arrestin family protein binding / G protein-coupled receptor internalization / response to morphine / Thrombin signalling through proteinase activated receptors (PARs) / positive regulation of intracellular signal transduction / mitogen-activated protein kinase kinase binding / regulation of heart contraction / positive regulation of Rho protein signal transduction / clathrin binding / negative regulation of Notch signaling pathway / stress fiber assembly / pseudopodium / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of interleukin-6 production / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of receptor internalization / positive regulation of vasoconstriction / phototransduction / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / endocytic vesicle / asymmetric synapse / immunoglobulin complex, circulating / immunoglobulin receptor binding / activation of adenylate cyclase activity / axon terminus / clathrin-coated pit / cellular response to hormone stimulus / negative regulation of protein ubiquitination / insulin-like growth factor receptor binding / visual perception / presynaptic modulation of chemical synaptic transmission / GTPase activator activity / complement activation, classical pathway / negative regulation of protein phosphorylation / peptide binding / clathrin-coated endocytic vesicle membrane / positive regulation of protein ubiquitination / response to cytokine / antigen binding / G protein-coupled receptor binding / nuclear estrogen receptor binding / phosphoprotein binding / response to virus / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G protein-coupled acetylcholine receptor signaling pathway / negative regulation of ERK1 and ERK2 cascade / Vasopressin regulates renal water homeostasis via Aquaporins / endocytosis / Cargo recognition for clathrin-mediated endocytosis / positive regulation of peptidyl-serine phosphorylation / Clathrin-mediated endocytosis / protein transport / nervous system development / presynaptic membrane / antibacterial humoral response / basolateral plasma membrane / G alpha (i) signalling events / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / G alpha (s) signalling events / chemical synaptic transmission / postsynaptic membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of apoptotic process Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Rattus norvegicus (Norway rat) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | |||||||||
Authors | Staus, D.P. / Hu, H. / Robertson, M.J. / Kleinhenz, A.L.W. / Wingler, L.M. / Capel, W.D. / Latorraca, N.R. / Lefkowitz, R.J. / Skiniotis, G. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nature / Year: 2020 Title: Structure of the M2 muscarinic receptor-β-arrestin complex in a lipid nanodisc. Authors: Dean P Staus / Hongli Hu / Michael J Robertson / Alissa L W Kleinhenz / Laura M Wingler / William D Capel / Naomi R Latorraca / Robert J Lefkowitz / Georgios Skiniotis / Abstract: After activation by an agonist, G-protein-coupled receptors (GPCRs) recruit β-arrestin, which desensitizes heterotrimeric G-protein signalling and promotes receptor endocytosis. Additionally, β- ...After activation by an agonist, G-protein-coupled receptors (GPCRs) recruit β-arrestin, which desensitizes heterotrimeric G-protein signalling and promotes receptor endocytosis. Additionally, β-arrestin directly regulates many cell signalling pathways that can induce cellular responses distinct from that of G proteins. In contrast to G proteins, for which there are many high-resolution structures in complex with GPCRs, the molecular mechanisms underlying the interaction of β-arrestin with GPCRs are much less understood. Here we present a cryo-electron microscopy structure of β-arrestin 1 (βarr1) in complex with M2 muscarinic receptor (M2R) reconstituted in lipid nanodiscs. The M2R-βarr1 complex displays a multimodal network of flexible interactions, including binding of the N domain of βarr1 to phosphorylated receptor residues and insertion of the finger loop of βarr1 into the M2R seven-transmembrane bundle, which adopts a conformation similar to that in the M2R-heterotrimeric G protein complex. Moreover, the cryo-electron microscopy map reveals that the C-edge of βarr1 engages the lipid bilayer. Through atomistic simulations and biophysical, biochemical and cellular assays, we show that the C-edge is critical for stable complex formation, βarr1 recruitment, receptor internalization, and desensitization of G-protein activation. Taken together, these data suggest that the cooperative interactions of β-arrestin with both the receptor and the phospholipid bilayer contribute to its functional versatility. | |||||||||
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 | 6u1n.cif.gz | 163.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u1n.ent.gz | 119.8 KB | Display | PDB format |
PDBx/mmJSON format | 6u1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6u1n_validation.pdf.gz | 837.7 KB | Display | wwPDB validaton report |
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Full document | 6u1n_full_validation.pdf.gz | 856.3 KB | Display | |
Data in XML | 6u1n_validation.xml.gz | 30.9 KB | Display | |
Data in CIF | 6u1n_validation.cif.gz | 45.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/6u1n ftp://data.pdbj.org/pub/pdb/validation_reports/u1/6u1n | HTTPS FTP |
-Related structure data
Related structure data | 20612MC 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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1 |
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-Components
#1: Protein | Mass: 56616.176 Da / Num. of mol.: 1 / Fragment: M2 UNP residues 2-466 + V2 UNP residues 343-371 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHRM2, AVPR2, ADHR, DIR, DIR3, V2R / Production host: Homo sapiens (human) / References: UniProt: P08172, UniProt: P30518 |
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#2: Protein | Mass: 45017.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arrb1 / Production host: Escherichia coli (E. coli) / References: UniProt: P29066 |
#3: Antibody | Mass: 25512.354 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: V9HW68 |
#4: Antibody | Mass: 23435.064 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z3Y4 |
#5: Chemical | ChemComp-2CU / |
Has ligand of interest | N |
-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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Buffer solution | pH: 7.4 | |||||||||||||||||||||||||||||||||||
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||
Specimen support | Details: unspecified | |||||||||||||||||||||||||||||||||||
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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 47169 X / Calibrated magnification: 47169 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.15rc3_3435: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 11700000 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145618 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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