+Open data
-Basic information
Entry | Database: PDB / ID: 8jpc | ||||||
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Title | cryo-EM structure of NTSR1-GRK2-Galpha(q) complexes 2 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Biased signaling | ||||||
Function / homology | Function and homology information Calmodulin induced events / beta-adrenergic-receptor kinase / negative regulation of the force of heart contraction by chemical signal / negative regulation of relaxation of smooth muscle / Activation of SMO / G protein-coupled neurotensin receptor activity / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / inositol phosphate catabolic process / Edg-2 lysophosphatidic acid receptor binding ...Calmodulin induced events / beta-adrenergic-receptor kinase / negative regulation of the force of heart contraction by chemical signal / negative regulation of relaxation of smooth muscle / Activation of SMO / G protein-coupled neurotensin receptor activity / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / inositol phosphate catabolic process / Edg-2 lysophosphatidic acid receptor binding / alpha-2A adrenergic receptor binding / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / symmetric synapse / D-aspartate import across plasma membrane / positive regulation of gamma-aminobutyric acid secretion / negative regulation of striated muscle contraction / desensitization of G protein-coupled receptor signaling pathway / Cargo recognition for clathrin-mediated endocytosis / positive regulation of protein localization to cilium / PLC beta mediated events / entrainment of circadian clock / regulation of the force of heart contraction / phospholipase C-activating dopamine receptor signaling pathway / regulation of platelet activation / regulation of membrane depolarization / positive regulation of arachidonate secretion / L-glutamate import across plasma membrane / phototransduction, visible light / regulation of respiratory gaseous exchange / positive regulation of inhibitory postsynaptic potential / G protein-coupled receptor internalization / positive regulation of smoothened signaling pathway / negative regulation of release of sequestered calcium ion into cytosol / negative regulation of systemic arterial blood pressure / positive regulation of glutamate secretion / glutamate receptor signaling pathway / regulation of canonical Wnt signaling pathway / G alpha (s) signalling events / G alpha (q) signalling events / positive regulation of inositol phosphate biosynthetic process / temperature homeostasis / response to lipid / action potential / detection of temperature stimulus involved in sensory perception of pain / neuropeptide signaling pathway / photoreceptor outer segment / regulation of signal transduction / cardiac muscle contraction / GTPase activator activity / G-protein beta/gamma-subunit complex binding / Peptide ligand-binding receptors / adult locomotory behavior / positive regulation of release of sequestered calcium ion into cytosol / dendritic shaft / learning / cell projection / G protein-coupled receptor binding / G protein-coupled receptor activity / intracellular protein transport / adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of protein kinase activity / Thromboxane signalling through TP receptor / terminal bouton / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / cytoplasmic side of plasma membrane / ADP signalling through P2Y purinoceptor 1 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / heterotrimeric G-protein complex / blood coagulation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Thrombin signalling through proteinase activated receptors (PARs) / presynapse / peptidyl-serine phosphorylation / G alpha (q) signalling events / nuclear membrane / chemical synaptic transmission / perikaryon / postsynapse / dendritic spine / protein stabilization / protein kinase activity / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / membrane raft / protein phosphorylation / lysosomal membrane / GTPase activity / synapse / GTP binding / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular exosome / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Bos taurus (cattle) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 Å | ||||||
Authors | Duan, J. / Liu, H. / Zhao, F. / Yuan, Q. / Ji, Y. / Xu, H.E. | ||||||
Funding support | China, 1items
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Citation | Journal: Nature / Year: 2023 Title: GPCR activation and GRK2 assembly by a biased intracellular agonist. Authors: Jia Duan / Heng Liu / Fenghui Zhao / Qingning Yuan / Yujie Ji / Xiaoqing Cai / Xinheng He / Xinzhu Li / Junrui Li / Kai Wu / Tianyu Gao / Shengnan Zhu / Shi Lin / Ming-Wei Wang / Xi Cheng / ...Authors: Jia Duan / Heng Liu / Fenghui Zhao / Qingning Yuan / Yujie Ji / Xiaoqing Cai / Xinheng He / Xinzhu Li / Junrui Li / Kai Wu / Tianyu Gao / Shengnan Zhu / Shi Lin / Ming-Wei Wang / Xi Cheng / Wanchao Yin / Yi Jiang / Dehua Yang / H Eric Xu / Abstract: Phosphorylation of G-protein-coupled receptors (GPCRs) by GPCR kinases (GRKs) desensitizes G-protein signalling and promotes arrestin signalling, which is also modulated by biased ligands. The ...Phosphorylation of G-protein-coupled receptors (GPCRs) by GPCR kinases (GRKs) desensitizes G-protein signalling and promotes arrestin signalling, which is also modulated by biased ligands. The molecular assembly of GRKs on GPCRs and the basis of GRK-mediated biased signalling remain largely unknown owing to the weak GPCR-GRK interactions. Here we report the complex structure of neurotensin receptor 1 (NTSR1) bound to GRK2, Gα and the arrestin-biased ligand SBI-553. The density map reveals the arrangement of the intact GRK2 with the receptor, with the N-terminal helix of GRK2 docking into the open cytoplasmic pocket formed by the outward movement of the receptor transmembrane helix 6, analogous to the binding of the G protein to the receptor. SBI-553 binds at the interface between GRK2 and NTSR1 to enhance GRK2 binding. The binding mode of SBI-553 is compatible with arrestin binding but clashes with the binding of Gα protein, thus providing a mechanism for its arrestin-biased signalling capability. In sum, our structure provides a rational model for understanding the details of GPCR-GRK interactions and GRK2-mediated biased signalling. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jpc.cif.gz | 246.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jpc.ent.gz | 184.9 KB | Display | PDB format |
PDBx/mmJSON format | 8jpc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jpc_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8jpc_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8jpc_validation.xml.gz | 47.1 KB | Display | |
Data in CIF | 8jpc_validation.cif.gz | 68 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/8jpc ftp://data.pdbj.org/pub/pdb/validation_reports/jp/8jpc | HTTPS FTP |
-Related structure data
Related structure data | 36475MC 8jpbC 8jpdC 8jpeC 8jpfC 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
-Protein/peptide , 1 types, 1 molecules L
#1: Protein/peptide | Mass: 819.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Protein , 3 types, 3 molecules RGQ
#2: Protein | Mass: 46307.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NTSR1, NTRR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P30989 |
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#3: Protein | Mass: 79644.727 Da / Num. of mol.: 1 / Mutation: A292P,R295I,S455D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GRK2, ADRBK1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P21146, beta-adrenergic-receptor kinase |
#4: Protein | Mass: 41282.895 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNAQ, GAQ / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P50148 |
-Non-polymers , 5 types, 5 molecules
#5: Chemical | ChemComp-SRW / |
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#6: Chemical | ChemComp-STU / |
#7: Chemical | ChemComp-GDP / |
#8: Chemical | ChemComp-MG / |
#9: Chemical | ChemComp-ALF / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: NTSR1-GRK2-Galpha(q) complexes 2 / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.4 |
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: FLOOD BEAM |
Electron lens | Mode: DARK FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 233943 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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