8XUM | pdb_00008xum

Structure of LGR4 with RSPO2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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

Cryo-EM structure of the full-length LGR4-RSPOs complex and a targeting nanobody for anti-obesity therapy.

Zhang, Z.Wang, L.Qiao, H.Jiang, H.Guo, S.Li, Y.Zhang, N.Geng, T.Cui, Q.Lan, Z.Hong, J.Gu, W.Liu, R.Ning, G.Li, J.Wang, J.Geng, Y.

(2025) Nat Commun 16: 8406-8406

  • DOI: https://doi.org/10.1038/s41467-025-63410-5
  • Primary Citation of Related Structures:  
    8XT9, 8XUM

  • PubMed Abstract: 

    Obesity poses a substantial threat to human health but lacks effective management. Recent advancements in large-scale deep sequencing and cryo-electron microscopy (cryo-EM) have transformed drug discovery paradigms. Leveraging prior genetics investigation, we pinpointed Leucine-rich repeat-containing G protein-coupled receptor 4 (LGR4) as a promising target for combating obesity. Here, we present cryo-EM structures of full-length LGR4 alone and in complex with RSPO2(FU). Notably, we develop an inhibitory nanobody (NB21) that blocks the binding of RSPO1/2 to LGR4, and we also determine the structure of the LGR4-NB21 complex. NB21-mFc (NB21 fused with mouse IgG2) effectively inhibits the canonical Wnt signaling pathway, thereby enhancing mitochondrial respiration and thermogenesis in beige adipocytes. In vivo, NB21-mFc increases energy expenditure by promoting the browning of white fat, conferring resistance to both diet-induced and genetic (ob/ob) obesity. Furthermore, LGR4 deficiency abolishes the effects of NB21-mFc in boosting the browning program and subsequent weight reduction. In summary, our study unveils structural insights into the LGR4-RSPOs and LGR4-NB21 complexes, paving the way for the development of an LGR4-targeting nanobody for weight loss.


  • Organizational Affiliation
    • Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MB52A [auth C]110Camelus bactrianusMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine-rich repeat-containing G-protein coupled receptor 4B [auth A]951Homo sapiensMutation(s): 0 
Gene Names: LGR4GPR48
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXB1 (Homo sapiens)
Explore Q9BXB1 
Go to UniProtKB:  Q9BXB1
PHAROS:  Q9BXB1
GTEx:  ENSG00000205213 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BXB1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
R-spondin-2C [auth B]243Homo sapiensMutation(s): 0 
Gene Names: RSPO2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q6UXX9 (Homo sapiens)
Explore Q6UXX9 
Go to UniProtKB:  Q6UXX9
PHAROS:  Q6UXX9
GTEx:  ENSG00000147655 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6UXX9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release
  • Version 1.1: 2025-12-24
    Changes: Data collection, Database references