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 8XT9 | pdb_00008xt9

structure of LGR4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8XT9

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 Related Structures: 
    8XT9, 8XUM, 9S37

  • 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.

Macromolecule Content 

  • Total Structure Weight: 116.57 kDa 
  • Atom Count: 6,479 
  • Modeled Residue Count: 842 
  • Deposited Residue Count: 1,061 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Leucine-rich repeat-containing G-protein coupled receptor 4A [auth C]951Homo sapiensMutation(s): 0 
Gene Names: LGR4, GPR48
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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
MB52B [auth A]110Camelus bactrianusMutation(s): 0 
UniProt
Find proteins for A0A0F6YEF6 (Camelus dromedarius)
Explore A0A0F6YEF6 
Go to UniProtKB:  A0A0F6YEF6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0F6YEF6
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



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