8JPE | pdb_00008jpe

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

• PDB DOI: https://doi.org/10.2210/pdb8JPE/pdb
• EM Map EMD-36477: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• 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: 2.91 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: 41.85 kDa 
• Atom Count: 2,189 
• Modeled Residue Count: 317 
• Deposited Residue Count: 353 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(q) subunit alpha	A [auth Q]	353	Homo sapiens	Mutation(s): 0  Gene Names: GNAQ, GAQ EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P50148 (Homo sapiens) Explore P50148  Go to UniProtKB:  P50148
PHAROS:  P50148 GTEx:  ENSG00000156052

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	B [auth Q]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
ALF (Subject of Investigation/LOI)	D [auth Q]	TETRAFLUOROALUMINATE ION Al F4 UYOMQIYKOOHAMK-UHFFFAOYSA-J
MG (Subject of Investigation/LOI)	C [auth Q]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.91 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
• Version 1.3: 2026-08-12
  Type: Remediation
  Reason: Metalloprotein remediation
  Changes: Data collection, Derived calculations, Structure summary