+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-20612 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | GPCR-Beta arrestin structure in lipid bilayer | |||||||||
![]() | GPCR-Beta arrestin structure in lipid bilayer | |||||||||
![]() |
| |||||||||
![]() | Arrestin / GPCR / complex / signaling / SIGNALING PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | ![]() V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / TGFBR3 regulates TGF-beta signaling / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / sensory perception of touch / G alpha (s) signalling events / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin ...V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / TGFBR3 regulates TGF-beta signaling / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / sensory perception of touch / G alpha (s) signalling events / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / regulation of inositol trisphosphate biosynthetic process / alpha-1B adrenergic receptor binding / follicle-stimulating hormone signaling pathway / protein phosphorylated amino acid binding / Lysosome Vesicle Biogenesis / angiotensin receptor binding / Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / AP-2 adaptor complex binding / Ub-specific processing proteases / cholinergic synapse / MAP2K and MAPK activation / Golgi Associated Vesicle Biogenesis / hemostasis / telencephalon development / Cargo recognition for clathrin-mediated endocytosis / clathrin adaptor activity / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / Clathrin-mediated endocytosis / negative regulation of interleukin-8 production / regulation of smooth muscle contraction / regulation of G protein-coupled receptor signaling pathway / G protein-coupled receptor internalization / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / arrestin family protein binding / Thrombin signalling through proteinase activated receptors (PARs) / response to morphine / mitogen-activated protein kinase kinase binding / clathrin binding / stress fiber assembly / regulation of heart contraction / positive regulation of Rho protein signal transduction / pseudopodium / positive regulation of systemic arterial blood pressure / negative regulation of interleukin-6 production / positive regulation of intracellular signal transduction / positive regulation of receptor internalization / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / negative regulation of Notch signaling pathway / endocytic vesicle / phototransduction / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of vasoconstriction / activation of adenylate cyclase activity / cellular response to hormone stimulus / insulin-like growth factor receptor binding / clathrin-coated pit / positive regulation of protein ubiquitination / response to cytokine / negative regulation of protein ubiquitination / presynaptic modulation of chemical synaptic transmission / GTPase activator activity / nuclear estrogen receptor binding / phosphoprotein binding / G protein-coupled receptor binding / clathrin-coated endocytic vesicle membrane / negative regulation of ERK1 and ERK2 cascade / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / response to virus / G protein-coupled acetylcholine receptor signaling pathway / positive regulation of protein phosphorylation / endocytosis / Vasopressin regulates renal water homeostasis via Aquaporins / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / nervous system development / protein transport / presynapse / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / G alpha (i) signalling events / regulation of apoptotic process / G alpha (s) signalling events / basolateral plasma membrane / molecular adaptor activity / chemical synaptic transmission / dendritic spine / proteasome-mediated ubiquitin-dependent protein catabolic process / negative regulation of neuron apoptotic process / transmembrane transporter binding / postsynaptic membrane / transcription coactivator activity / positive regulation of ERK1 and ERK2 cascade / protein ubiquitination / endosome / positive regulation of MAPK cascade / postsynaptic density / ciliary basal body Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
![]() | Staus DP / Hu H | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 49.4 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 17.9 KB 17.9 KB | Display Display | ![]() |
Images | ![]() | 96.1 KB | ||
Filedesc metadata | ![]() | 6.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 466.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 465.8 KB | Display | |
Data in XML | ![]() | 5.8 KB | Display | |
Data in CIF | ![]() | 6.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6u1nMC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | GPCR-Beta arrestin structure in lipid bilayer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-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). |
---|---|
Components |
|
-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 |
---|
-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. |
---|---|
Source (natural) | Organism: ![]() |
-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 |
---|---|
Source (natural) | Organism: ![]() ![]() |
-Supramolecule #4: Antibody Fragment (Fab30)
Supramolecule | Name: Antibody Fragment (Fab30) / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4 |
---|---|
Source (natural) | Organism: ![]() |
-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 |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 56.616176 KDa |
Recombinant expression | Organism: ![]() |
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 UniProtKB: Muscarinic acetylcholine receptor M2, Vasopressin V2 receptor |
-Macromolecule #2: Beta-arrestin-1
Macromolecule | Name: Beta-arrestin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 45.01718 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 UniProtKB: Beta-arrestin-1 |
-Macromolecule #3: Fab30 heavy chain
Macromolecule | Name: Fab30 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 25.512354 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 UniProtKB: Epididymis luminal protein 214 |
-Macromolecule #4: Fab30 light chain
Macromolecule | Name: Fab30 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 23.435064 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 UniProtKB: Ig-like domain-containing protein |
-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 |
---|---|
Molecular weight | Theoretical: 437.944 Da |
Chemical component information | ![]() ChemComp-2CU: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 2 mg/mL |
---|---|
Buffer | pH: 7.4 |
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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: ![]() |
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 |
---|---|
Output model | ![]() PDB-6u1n: |