8JPD | pdb_00008jpd

Focused refinement structure of GRK2 in NTSR1-GRK2-Galpha(q) complexes

• PDB DOI: https://doi.org/10.2210/pdb8JPD/pdb
• EM Map EMD-36476: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Bos taurus
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2023-06-11 Released: 2023-08-09 
• Deposition Author(s): Duan, J., Liu, H., Zhao, F., Yuan, Q., Ji, Y., Xu, H.E.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.81 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

GPCR activation and GRK2 assembly by a biased intracellular agonist.

Duan, J., Liu, H., Zhao, F., Yuan, Q., Ji, Y., Cai, X., He, X., Li, X., Li, J., Wu, K., Gao, T., Zhu, S., Lin, S., Wang, M.W., Cheng, X., Yin, W., Jiang, Y., Yang, D., Xu, H.E.

(2023) Nature 620: 676-681

• PubMed: 37532940 
• DOI: https://doi.org/10.1038/s41586-023-06395-9
• Primary Citation Related Structures: 
  8JPB, 8JPC, 8JPD, 8JPE, 8JPF


• PubMed 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 ^1-6 . 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 _q and the arrestin-biased ligand SBI-553 ⁷ . 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 _q 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.

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Organizational Affiliation: 
• State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. [e-mail].
Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
University of Chinese Academy of Sciences, Beijing, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Research Center for Deepsea Bioresources, Sanya, Hainan, China.
Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China.
Lingang Laboratory, Shanghai, China.
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. [e-mail].
Research Center for Deepsea Bioresources, Sanya, Hainan, China. [e-mail].
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 80.11 kDa 
• Atom Count: 5,198 
• Modeled Residue Count: 658 
• Deposited Residue Count: 688 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-adrenergic receptor kinase 1	A [auth G]	688	Bos taurus	Mutation(s): 3  Gene Names: GRK2, ADRBK1 EC: 2.7.11.15 (PDB Primary Data), 2.7.11.16 (UniProt)
UniProt
Find proteins for P21146 (Bos taurus) Explore P21146  Go to UniProtKB:  P21146

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STU (Subject of Investigation/LOI)	B [auth G]	STAUROSPORINE C28 H26 N4 O3 HKSZLNNOFSGOKW-FYTWVXJKSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
STU	BindingDB:  8JPD	IC50: 1.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.81 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-09 
Deposition Author(s): Duan, J., Liu, H., Zhao, F., Yuan, Q., Ji, Y., Xu, H.E.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2023-08-09
  Type: Initial release
  
• Version 1.1: 2023-08-16
  Changes: Data collection, Database references
• Version 1.2: 2023-08-30
  Changes: Database references