8JPC

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


This is version 1.3 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 of 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NTS(8-13)A [auth L]6synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Neurotensin receptor type 1B [auth R]418Homo sapiensMutation(s): 0 
Gene Names: NTSR1NTRR
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 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30989
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-adrenergic receptor kinase 1C [auth G]688Bos taurusMutation(s): 3 
Gene Names: GRK2ADRBK1
EC: 2.7.11.15
Membrane Entity: Yes 
UniProt
Find proteins for P21146 (Bos taurus)
Explore P21146 
Go to UniProtKB:  P21146
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UniProt GroupP21146
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(q) subunit alphaD [auth Q]353Homo sapiensMutation(s): 0 
Gene Names: GNAQGAQ
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 
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UniProt GroupP50148
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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
Experimental Data & Validation

Experimental Data

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

Structure Validation

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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