9UYN | pdb_00009uyn

Cryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to beta-arrestin 1 in ligand-free state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9UYN

This is version 1.1 of the entry. See complete history

Literature

Noncanonical agonist-dependent and -independent arrestin recruitment of GPR1.

Cai, H.Lin, X.Zhao, L.He, M.Yu, J.Zhang, B.Ma, Y.Chang, X.Tang, Y.Luo, T.Jiang, J.Ma, M.Song, W.Ma, L.Chu, X.Yi, C.Chen, K.Han, S.Xie, C.Shui, W.Zhao, Q.Zhu, Y.Wu, B.

(2025) Science 390: eadt8794-eadt8794

  • DOI: https://doi.org/10.1126/science.adt8794
  • Primary Citation Related Structures: 
    9UYH, 9UYI, 9UYJ, 9UYL, 9UYM, 9UYN

  • PubMed Abstract: 

    G protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptors have diverse signaling properties with differential preferences for downstream pathways. Certain receptors, such as the chemerin receptor GPR1, undergo arrestin-mediated internalization but weak G protein signaling. However, the mechanisms of this unusual signaling pattern and its physiological relevance are unclear. We report the structures of GPR1 bound to chemerin and β-arrestin 1 or β-arrestin 2 and an agonist-free GPR1-β-arrestin 1 complex. Upon agonist stimulation, the receptor binds the two arrestins in distinct interaction patterns, which may account for their differential cellular responses. Agonist-independent internalization was mediated by an inactive, constitutively phosphorylated GPR1 that accommodates β-arrestin 1 in an unconventional pocket together with a fatty acid, which potentially provides a basis for GPR1 modulating lipid accumulation in lipid-overloaded adipocytes.


  • Organizational Affiliation
    • School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.

Macromolecule Content 

  • Total Structure Weight: 129.79 kDa 
  • Atom Count: 7,503 
  • Modeled Residue Count: 967 
  • Deposited Residue Count: 1,155 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chemerin-like receptor 2,Vasopressin V2 receptorA [auth R]414Homo sapiensMutation(s): 1 
Gene Names: CMKLR2GPR1AVPR2ADHRDIRDIR3V2R
UniProt & NIH Common Fund Data Resources
Find proteins for P30518 (Homo sapiens)
Explore P30518 
Go to UniProtKB:  P30518
PHAROS:  P30518
GTEx:  ENSG00000126895 
Find proteins for P46091 (Homo sapiens)
Explore P46091 
Go to UniProtKB:  P46091
PHAROS:  P46091
GTEx:  ENSG00000183671 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP30518P46091
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-arrestin-1B [auth A]376Homo sapiensMutation(s): 9 
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49407
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody 32C [auth B]120Escherichia phage EcSzw-2Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Single-chain fragment variable 30 (scFv30)D [auth C]245Homo sapiensMutation(s): 0 

Small Molecules

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

Query on PAM



Download:Ideal Coordinates CCD File
E [auth R]PALMITOLEIC ACID
C16 H30 O2
SECPZKHBENQXJG-FPLPWBNLSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A [auth R]L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A [auth R]L-PEPTIDE LINKINGC4 H10 N O6 PTHR

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2_3874

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82121005
National Natural Science Foundation of China (NSFC)China32401012

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2025-12-03
    Changes: Data collection, Database references