8HSV

The structure of rat beta-arrestin1 in complex with a rat Mdm2 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

GPCR targeting of E3 ubiquitin ligase MDM2 by inactive beta-arrestin.

Yun, Y.Yoon, H.J.Jeong, Y.Choi, Y.Jang, S.Chung, K.Y.Lee, H.H.

(2023) Proc Natl Acad Sci U S A 120: e2301934120-e2301934120

  • DOI: https://doi.org/10.1073/pnas.2301934120
  • Primary Citation of Related Structures:  
    8HST, 8HSV

  • PubMed Abstract: 

    E3 ubiquitin ligase Mdm2 facilitates β-arrestin ubiquitination, leading to the internalization of G protein-coupled receptors (GPCRs). In this process, β-arrestins bind to Mdm2 and recruit it to the receptor; however, the molecular architecture of the β-arrestin-Mdm2 complex has not been elucidated yet. Here, we identified the β-arrestin-binding region (ABR) on Mdm2 and solved the crystal structure of β-arrestin1 in complex with Mdm2 ABR peptide. The acidic residues of Mdm2 ABR bind to the positively charged concave side of the β-arrestin1 N-domain. The C-tail of β-arrestin1 is still bound to the N-domain, indicating that Mdm2 binds to the inactive state of β-arrestin1, whereas the phosphorylated C-terminal tail of GPCRs binds to activate β-arrestins. The overlapped binding site of Mdm2 and GPCR C-tails on β-arrestin1 suggests that the binding of GPCR C-tails might trigger the release of Mdm2. Moreover, hydrogen/deuterium exchange experiments further show that Mdm2 ABR binding to β-arrestin1 induces the interdomain interface to be more dynamic and uncouples the IP 6 -induced oligomer of β-arrestin1. These results show how the E3 ligase, Mdm2, interacts with β-arrestins to promote the internalization of GPCRs.


  • Organizational Affiliation

    Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-arrestin-1A,
C [auth B]
414Rattus norvegicusMutation(s): 7 
Gene Names: Arrb1
UniProt
Find proteins for P29066 (Rattus norvegicus)
Explore P29066 
Go to UniProtKB:  P29066
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UniProt GroupP29066
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
peptide from E3 ubiquitin-protein ligase Mdm2B [auth E],
D [auth F]
18Rattus norvegicusMutation(s): 0 
EC: 2.3.2.27
UniProt
Find proteins for A0A8I6G5V3 (Rattus norvegicus)
Explore A0A8I6G5V3 
Go to UniProtKB:  A0A8I6G5V3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8I6G5V3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.673α = 90
b = 80.673β = 90
c = 173.555γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-19
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection