9DNG | pdb_00009dng

Structure of rat beta-arrestin 1 by fiducial-assisted cryo-EM

• PDB DOI: https://doi.org/10.2210/pdb9DNG/pdb
• EM Map EMD-47040: EMDB EMDataResource

• Classification: SIGNALING PROTEIN/Immune System
• Organism(s): Homo sapiens, Rattus norvegicus
• Expression System: Escherichia coli, Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2024-09-17 Released: 2025-01-22 
• Deposition Author(s): Pakharukova, N., Kahsai, A.W., Masoudi, A., Lefkowitz, R.J.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), Human Frontier Science Program (HFSP), European Molecular Biology Organization (EMBO)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.52 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

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 

• PubMed: 42343124 
• 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.

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Organizational Affiliation: 
• Department of Medicine, Duke University Medical Center, Durham, NC, USA. [e-mail].
Department of Medicine, Duke University Medical Center, Durham, NC, USA.
Department of Surgery, Henry Ford Hospital, Detroit, MI, USA.
Duke University School of Medicine, Duke University Medical Center, Durham, NC, USA.
Cedars-Sinai Medical Center, Los Angeles, CA, USA.
US Department of Energy, National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
Department of Biochemistry, Duke University Medical Center, Durham, NC, USA.
Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, USA.
Department of Cell Biology, Duke University Medical Center, Durham, NC, USA.
Departments of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Computational Chemistry and Molecular Biophysics Section, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, MD, USA.
Department of Medicine, Duke University Medical Center, Durham, NC, USA. [e-mail].
Department of Biochemistry, Duke University Medical Center, Durham, NC, USA. [e-mail].
Department of Chemistry, Duke University Medical Center, Durham, NC, USA. [e-mail].
Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 102.84 kDa 
• Atom Count: 5,252 
• Modeled Residue Count: 675 
• Deposited Residue Count: 931 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-BRIL Fab Heavy chain	A [auth H]	225	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-BRIL Fab LIGHT chain	B [auth L]	212	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-arrestin-1,Soluble cytochrome b562	C [auth A]	494	Rattus norvegicus	Mutation(s): 10  Gene Names: Arrb1, cybC
UniProt
Find proteins for P29066 (Rattus norvegicus) Explore P29066  Go to UniProtKB:  P29066

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.52 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.4.1
MODEL REFINEMENT	PHENIX	1.20.1-4487

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Pakharukova, N., Kahsai, A.W., Masoudi, A., Lefkowitz, R.J.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL016037
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	T32HL007101
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL16037-45S1
Human Frontier Science Program (HFSP)	France	LT000174/2018
European Molecular Biology Organization (EMBO)	European Union	ALTF 1071-2017

Revision History  

• 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