9UYM | pdb_00009uym

Composite map of the G protein-coupled receptor 1 (GPR1) bound to chemerin and beta-arrestin 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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 of 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.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Retinoic acid receptor responder protein 2A [auth L]153Homo sapiensMutation(s): 0 
Gene Names: RARRES2TIG2
UniProt & NIH Common Fund Data Resources
Find proteins for Q99969 (Homo sapiens)
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Go to UniProtKB:  Q99969
PHAROS:  Q99969
GTEx:  ENSG00000106538 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99969
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 32120Escherichia phage EcSzw-2Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Single-chain fragment variable 30 (scFv30)245Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-arrestin-2,Beta-arrestin-1D [auth A]369Homo sapiensMutation(s): 8 
Gene Names: ARRB2ARB2ARR2ARRB1ARR1
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Find proteins for P32121 (Homo sapiens)
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PHAROS:  P32121
GTEx:  ENSG00000141480 
Find proteins for P49407 (Homo sapiens)
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PHAROS:  P49407
GTEx:  ENSG00000137486 
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UniProt GroupsP32121P49407
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Chemerin-like receptor 2,Vasopressin V2 receptorE [auth R]414Homo sapiensMutation(s): 0 
Gene Names: CMKLR2GPR1AVPR2ADHRDIRDIR3V2R
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Find proteins for P30518 (Homo sapiens)
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PHAROS:  P30518
GTEx:  ENSG00000126895 
Find proteins for P46091 (Homo sapiens)
Explore P46091 
Go to UniProtKB:  P46091
PHAROS:  P46091
GTEx:  ENSG00000183671 
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UniProt GroupsP30518P46091
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y01 (Subject of Investigation/LOI)
Query on Y01

Download Ideal Coordinates CCD File 
F [auth A]CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
E [auth R]L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
E [auth R]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2_3874

Structure Validation

View Full Validation Report



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