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 8JPC | pdb_00008jpc

cryo-EM structure of NTSR1-GRK2-Galpha(q) complexes 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8JPC

This is version 1.5 of the entry. See complete history. 

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

  • 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.


  • Organizational Affiliation: 
    • State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. duanjia@simm.ac.cn.

Macromolecule Content 

  • Total Structure Weight: 169.54 kDa 
  • Atom Count: 9,589 
  • Modeled Residue Count: 1,278 
  • Deposited Residue Count: 1,465 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NTS(8-13)A [auth L]6synthetic constructMutation(s): 0 
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Neurotensin receptor type 1B [auth R]418Homo sapiensMutation(s): 0 
Gene Names: NTSR1, NTRR
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P30989 (Homo sapiens)
Explore P30989 
Go to UniProtKB:  P30989
PHAROS:  P30989
GTEx:  ENSG00000101188 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30989
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-adrenergic receptor kinase 1C [auth G]688Bos taurusMutation(s): 3 
Gene Names: GRK2, ADRBK1
EC: 2.7.11.15 (PDB Primary Data), 2.7.11.16 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P21146 (Bos taurus)
Explore P21146 
Go to UniProtKB:  P21146
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21146
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(q) subunit alphaD [auth Q]353Homo sapiensMutation(s): 0 
Gene Names: GNAQ, GAQ
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P50148 (Homo sapiens)
Explore P50148 
Go to UniProtKB:  P50148
PHAROS:  P50148
GTEx:  ENSG00000156052 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50148
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
STU

Query on STU



Download:Ideal Coordinates CCD File
F [auth G]STAUROSPORINE
C28 H26 N4 O3
HKSZLNNOFSGOKW-FYTWVXJKSA-N
SRW

Query on SRW



Download:Ideal Coordinates CCD File
E [auth R]2-[{2-(1-fluorocyclopropyl)-4-[4-(2-methoxyphenyl)piperidin-1-yl]quinazolin-6-yl}(methyl)amino]ethan-1-ol
C26 H31 F N4 O2
BLWXTJQMEBQCIZ-UHFFFAOYSA-N
GDP
(Subject of Investigation/LOI)

Query on GDP



Download:Ideal Coordinates CCD File
G [auth Q]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ALF
(Subject of Investigation/LOI)

Query on ALF



Download:Ideal Coordinates CCD File
I [auth Q]TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
H [auth Q]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
STU BindingDB:  8JPC IC50: 1.1 (nM) from 1 assay(s)
SRW BindingDB:  8JPC EC50: min: 1.2, max: 500 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • 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: 2024-11-06
    Changes: Data collection, Structure summary
  • Version 1.4: 2025-06-25
    Changes: Data collection
  • Version 1.5: 2026-08-12
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Data collection, Derived calculations