+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20612 | |||||||||
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Title | GPCR-Beta arrestin structure in lipid bilayer | |||||||||
Map data | GPCR-Beta arrestin structure in lipid bilayer | |||||||||
Sample |
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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 | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Staus DP / Hu H / Robertson MJ / Kleinhenz ALW / Wingler LM / Capel WD / Latorraca NR / Lefkowitz RJ / Skiniotis G | |||||||||
Funding support | United States, 2 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20612.map.gz | 49.4 MB | EMDB map data format | |
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Header (meta data) | emd-20612-v30.xml emd-20612.xml | 18.8 KB 18.8 KB | Display Display | EMDB header |
Images | emd_20612.png | 96.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20612 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20612 | HTTPS FTP |
-Validation report
Summary document | emd_20612_validation.pdf.gz | 408.7 KB | Display | EMDB validaton report |
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Full document | emd_20612_full_validation.pdf.gz | 408.3 KB | Display | |
Data in XML | emd_20612_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | emd_20612_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20612 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20612 | HTTPS FTP |
-Related structure data
Related structure data | 6u1nMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_20612.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | GPCR-Beta arrestin structure in lipid bilayer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Phosphorylated human muscarinic acetylcholine receptor M2 in comp...
Entire | Name: Phosphorylated human muscarinic acetylcholine receptor M2 in complex with rat beta-arrestin1, stabilized by an antibody fragment (Fab30). |
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Components |
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-Supramolecule #1: Phosphorylated human muscarinic acetylcholine receptor M2 in comp...
Supramolecule | Name: Phosphorylated human muscarinic acetylcholine receptor M2 in complex with rat beta-arrestin1, stabilized by an antibody fragment (Fab30). type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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-Supramolecule #2: Phosphorylated human muscarinic acetylcholine receptor M2
Supramolecule | Name: Phosphorylated human muscarinic acetylcholine receptor M2 type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 Details: Phosphorylated M2R was generated by ligating a synthetic phosphopeptide derived from the vasopressin-2-receptor (V2Rpp) using the enzyme sortase. |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: Cysteine-free rat beta-arrestin 1 truncated at amino acid 393
Supramolecule | Name: Cysteine-free rat beta-arrestin 1 truncated at amino acid 393 type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Supramolecule #4: Antibody Fragment (Fab30)
Supramolecule | Name: Antibody Fragment (Fab30) / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Muscarinic acetylcholine receptor M2, Vasopressin V2 receptor chimera
Macromolecule | Name: Muscarinic acetylcholine receptor M2, Vasopressin V2 receptor chimera type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 56.616176 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DYKDDDDKNN STNSSNNSLA LTSPYKTFEV VFIVLVAGSL SLVTIIGNIL VMVSIKVNRH LQTVNNYFLF SLACADLIIG VFSMNLYTL YTVIGYWPLG PVVCDLWLAL DYVVSNASVM NLLIISFDRY FCVTKPLTYP VKRTTKMAGM MIAAAWVLSF I LWAPAILF ...String: DYKDDDDKNN STNSSNNSLA LTSPYKTFEV VFIVLVAGSL SLVTIIGNIL VMVSIKVNRH LQTVNNYFLF SLACADLIIG VFSMNLYTL YTVIGYWPLG PVVCDLWLAL DYVVSNASVM NLLIISFDRY FCVTKPLTYP VKRTTKMAGM MIAAAWVLSF I LWAPAILF WQFIVGVRTV EDGECYIQFF SNAAVTFGTA IAAFYLPVII MTVLYWHISR ASKSRIKKDK KEPVANQDPV SP SLVQGRI VKPNNNNMPS SDDGLEHNKI QNGKAPRDPV TENCVQGEEK ESSNDSTSVS AVASNMRDDE ITQDENTVST SLG HSKDEN SKQTCIRIGT KTPKSDSCTP TNTTVEVVGS SGQNGDEKQN IVARKIVKMT KQPAKKKPPP SREKKVTRTI LAIL LAFII TWAPYNVMVL INTFCAPCIP NTVWTIGYWL CYINSTINPA CYALCNATFK KTFKHLLMCH YKNIGATRLP ETGGG ARGR TPPSLGPQDE (SEP)C(TPO)(TPO)A(SEP)(SEP)(SEP)LA KDTSS |
-Macromolecule #2: Beta-arrestin-1
Macromolecule | Name: Beta-arrestin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 45.01718 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GSPEFPGRLG DKGTRVFKKA SPNGKLTVYL GKRDFVDHID LVDPVDGVVL VDPEYLKERR VYVTLTVAFR YGREDLDVLG LTFRKDLFV ANVQSFPPAP EDKKPLTRLQ ERLIKKLGEH AYPFTFEIPP NLPSSVTLQP GPEDTGKALG VDYEVKAFVA E NLEEKIHK ...String: GSPEFPGRLG DKGTRVFKKA SPNGKLTVYL GKRDFVDHID LVDPVDGVVL VDPEYLKERR VYVTLTVAFR YGREDLDVLG LTFRKDLFV ANVQSFPPAP EDKKPLTRLQ ERLIKKLGEH AYPFTFEIPP NLPSSVTLQP GPEDTGKALG VDYEVKAFVA E NLEEKIHK RNSVRLVIRK VQYAPERPGP QPTAETTRQF LMSDKPLHLE ASLDKEIYYH GEPISVNVHV TNNTNKTVKK IK ISVRQYA DIVLFNTAQY KVPVAMEEAD DTVAPSSTFS KVYTLTPFLA NNREKRGLAL DGKLKHEDTN LASSTLLREG ANR EILGII VSYKVKVKLV VSRGGLLGDL ASSDVAVELP FTLMHPKPKE EPPHREVPES ETPVDTNLIE LDTNDDDIVF EDFA R |
-Macromolecule #3: Fab30 heavy chain
Macromolecule | Name: Fab30 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 25.512354 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYSSSIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSRQFWYSG LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYSSSIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSRQFWYSG LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK THHHHHHHH |
-Macromolecule #4: Fab30 light chain
Macromolecule | Name: Fab30 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.435064 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-Macromolecule #5: 3-amino-5-chloro-N-cyclopropyl-4-methyl-6-[2-(4-methylpiperazin-1...
Macromolecule | Name: 3-amino-5-chloro-N-cyclopropyl-4-methyl-6-[2-(4-methylpiperazin-1-yl)-2-oxoethoxy]thieno[2,3-b]pyridine-2-carboxamide type: ligand / ID: 5 / Number of copies: 1 / Formula: 2CU |
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Molecular weight | Theoretical: 437.944 Da |
Chemical component information | ChemComp-2CU: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.4 |
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 47169 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 47169 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-6u1n: |