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 9UTO | pdb_00009uto

Cryo-EM structure of the oxytocin receptor bound to nanobody Nb2B1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9UTO

This is version 1.0 of the entry. See complete history. 

Literature

Discovery of an antagonist nanobody targeting the oxytocin receptor with tocolytic effect in mice.

Nie, J., Gao, K., Zhang, X., Meng, H., Li, Q., Zhang, X., Wu, Y., Zeng, H., Liu, W., Liu, L., Tan, L., Sun, X., Liu, X., Zhang, W.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-77680-0
  • Primary Citation Related Structures: 
    9UOT, 9UTO, 9UTP, 9UVQ

  • PubMed Abstract: 

    Preterm birth, defined as delivery before 37 completed weeks of gestation, poses significant risks to maternal and neonatal health. These risks include neonatal respiratory distress syndrome, intraventricular hemorrhage, long-term developmental challenges, and in severe cases, mortality. Addressing these issues, G protein-coupled receptor (GPCR)-mediated tocolysis has become a focal strategy in pharmaceutical research to mitigate preterm labor risks. Most GPCR drugs are small molecules, yet their tendency to cross the placental barrier and induce fetal toxicity presents a significant challenge. Antibody drugs, with minimal cell membrane permeability, offer a promising alternative. In this study, we leverage AI-driven protein design to enable nanobody screening and identify several nanobodies with antagonist activity against the oxytocin receptor, a key target for preterm birth therapeutics. One of these nanobodies demonstrates antagonist activity comparable to Atosiban, a commonly used clinical drug, while exhibiting higher subtype selectivity. Pharmacological and structural analyses reveal mechanisms distinct from small molecule antagonists. These findings expand the pharmacological potential of antibody drugs and introduce useful tools and perspectives for developing effective tocolytic agents.


  • Organizational Affiliation: 
    • Department of Obstetrics, Xiangya Hospital Central South University, Changsha, China.

Macromolecule Content 

  • Total Structure Weight: 53.75 kDa 
  • Atom Count: 2,949 
  • Modeled Residue Count: 404 
  • Deposited Residue Count: 487 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Oxytocin receptor361Homo sapiensMutation(s): 0 
Gene Names: OXTR
UniProt & NIH Common Fund Data Resources
Find proteins for P30559 (Homo sapiens)
Explore P30559 
Go to UniProtKB:  P30559
PHAROS:  P30559
GTEx:  ENSG00000180914 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30559
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nb2B1126Vicugna pacosMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32122041

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-28
    Type: Initial release