8ZYT | pdb_00008zyt

Cryo-EM structure of neurotensin receptor 1 in complex with beta-arrestin1 and SBI-553 (complex 3)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 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

Molecular mechanism of the arrestin-biased agonism of neurotensin receptor 1 by an intracellular allosteric modulator.

Sun, D.Li, X.Yuan, Q.Wang, Y.Shi, P.Zhang, H.Wang, T.Sun, W.Ling, S.Liu, Y.Lai, J.Xie, W.Yin, W.Liu, L.Xu, H.E.Tian, C.

(2025) Cell Res 35: 284-295

  • DOI: https://doi.org/10.1038/s41422-025-01095-7
  • Primary Citation of Related Structures:  
    8ZYT, 8ZYU, 8ZYY, 9M0D

  • PubMed Abstract: 

    Biased allosteric modulators (BAMs) of G protein-coupled receptors (GPCRs) have been at the forefront of drug discovery owing to their potential to selectively stimulate therapeutically relevant signaling and avoid on-target side effects. Although structures of GPCRs in complex with G protein or GRK in a BAM-bound state have recently been resolved, revealing that BAM can induce biased signaling by directly modulating interactions between GPCRs and these two transducers, no BAM-bound GPCR-arrestin complex structure has yet been determined, limiting our understanding of the full pharmacological profile of BAMs. Herein, we developed a chemical protein synthesis strategy to generate neurotensin receptor 1 (NTSR1) with defined hexa-phosphorylation at its C-terminus and resolved high-resolution cryo-EM structures (2.65-2.88 Å) of NTSR1 in complex with both β-arrestin1 and the BAM SBI-553. These structures revealed a unique "loop engagement" configuration of β-arrestin1 coupling to NTSR1 in the presence of SBI-553, markedly different from the typical "core engagement" configuration observed in the absence of BAMs. This configuration is characterized by the engagement of the intracellular loop 3 of NTSR1 with a cavity in the central crest of β-arrestin1, representing a previously unobserved, arrestin-selective conformation of GPCR. Our findings fill the critical knowledge gap regarding the regulation of GPCR-arrestin interactions and biased signaling by BAMs, which would advance the development of safer and more efficacious GPCR-targeted therapeutics.


  • Organizational Affiliation
    • Hefei National Laboratory for Physical Sciences at the Microscale, Joint Center for Biological Analytical Chemistry, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-arrestin-1A [auth B]402Homo sapiensMutation(s): 0 
Gene Names: ARRB1ARR1
UniProt & NIH Common Fund Data Resources
Find proteins for P49407 (Homo sapiens)
Explore P49407 
Go to UniProtKB:  P49407
PHAROS:  P49407
GTEx:  ENSG00000137486 
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UniProt GroupP49407
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab30 heavy chainB [auth D]260Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab30 light chainC [auth Q]235Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,Neurotensin receptor type 1D [auth R]557Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: cybCNTSR1NTRR
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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UniProt GroupP30989
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  • Reference Sequence

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
neurotensin peptide 8-13E [auth L]6Homo sapiensMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PIO
Query on PIO

Download Ideal Coordinates CCD File 
F [auth R][(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
C25 H49 O19 P3
XLNCEHRXXWQMPK-MJUMVPIBSA-N
SRW (Subject of Investigation/LOI)
Query on SRW

Download Ideal Coordinates CCD File 
G [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
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
D [auth R]L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
D [auth R]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 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)ChinaT2221005

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release
  • Version 1.1: 2025-04-16
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-28
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2025-07-23
    Changes: Data collection