9DNM | pdb_00009dnm

Structure of rat beta-arrestin 1 bound to allosteric inhibitor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9DNM

This is version 1.2 of the entry. See complete history

Literature

Small-molecule modulation of beta-arrestins.

Kahsai, A.W.Pakharukova, N.Kwon, H.Y.Shah, K.S.Del Real, C.T.Shreiber, B.N.Liang-Lin, J.G.Shim, P.J.Lee, M.A.Ngo, V.A.Schwalb, A.M.Pham, U.Chundi, A.Jiang, H.Flores-Espinoza, E.Liu, S.Nibley, P.C.Bassford, D.K.Hahn, H.Kunzle, C.A.Thomas, B.N.Kim, J.Zhou, Y.Wang, J.Zhang, X.Smith, J.S.Rein, L.A.M.Thomsen, A.R.B.Shenoy, S.K.Rajagopal, S.Shi, L.Ahn, S.Rockman, H.A.Masoudi, A.Lefkowitz, R.J.

(2026) Nature 

  • DOI: https://doi.org/10.1038/s41586-026-10683-5
  • Primary Citation Related Structures: 
    9DNG, 9DNM

  • PubMed Abstract: 

    β-Arrestins are multifunctional regulators of G-protein-coupled receptor (GPCR) signalling and orchestrate diverse downstream signalling events and physiological responses across the GPCR superfamily 1-3 . Although GPCR pharmacology has advanced to target orthosteric and allosteric sites, as well as G proteins and GPCR kinases, direct chemical tools to modulate β-arrestin activities have remained conspicuously absent. Here we report the identification of small-molecule inhibitors that selectively target β-arrestins and delineate their mechanism of action through integrated pharmacological, biochemical, biophysical and structural analyses. These inhibitors disrupt β-arrestin engagement with agonist-activated GPCRs, impairing desensitization, internalization and β-arrestin-dependent physiological functions while sparing G protein-receptor coupling. Cryo-electron microscopy, molecular dynamics simulations and structure-guided mutagenesis reveal that one modulator, Cmpd-5, engages a pocket within the central crest of β-arrestin1 formed by the middle, C and lariat loops, a critical receptor-binding interface, stabilizing a distinct conformation that is incompatible with full β-arrestin-receptor engagement. Together, these findings establish a mechanistic framework for β-arrestin modulation, reveal a novel allosteric site for structure-based drug design, and open new avenues for transducer-targeted, pathway-specific GPCR therapeutic agents.


  • Organizational Affiliation
    • Department of Medicine, Duke University Medical Center, Durham, NC, USA. alem@receptor-biol.duke.edu.

Macromolecule Content 

  • Total Structure Weight: 103.21 kDa 
  • Atom Count: 5,235 
  • Modeled Residue Count: 668 
  • Deposited Residue Count: 931 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
anti-BRIL Fab Heavy chainA [auth H]225Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
anti-BRIL Fab Light chainB [auth L]212Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-arrestin-1,Soluble cytochrome b562C [auth A]494Rattus norvegicusMutation(s): 10 
Gene Names: Arrb1cybC
UniProt
Find proteins for P29066 (Rattus norvegicus)
Explore P29066 
Go to UniProtKB:  P29066
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29066
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ODN
(Subject of Investigation/LOI)

Query on ODN



Download:Ideal Coordinates CCD File
D [auth A](1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14R,16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one
C20 H30 O6
RWELMBQGCLVKOE-ZJOCIWLNSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1-4487
RECONSTRUCTIONcryoSPARC4.4.1

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL016037
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesT32HL007101
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL16037-45S1
Human Frontier Science Program (HFSP)FranceLT000174/2018
European Molecular Biology Organization (EMBO)European UnionALTF 1071-2017

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection, Database references
  • Version 1.2: 2026-07-15
    Changes: Data collection, Database references