9U80 | pdb_00009u80

Cryo-EM structure of conivaptan-bound human vasopressin V2 receptor complex with Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural insights into antagonist recognition by the vasopressin V2 receptor.

Zhang, T.Liu, H.You, C.Zhang, Y.Xu, Y.Pan, B.Wu, C.Jin, S.Yin, Y.L.Wu, K.Chen, Y.Sun, H.Si, Y.Tan, Y.Yin, W.Xu, H.E.Guo, D.Jiang, Y.

(2025) Nat Commun 16: 9734-9734

  • DOI: https://doi.org/10.1038/s41467-025-64735-x
  • Primary Citation of Related Structures:  
    9U80, 9U81

  • PubMed Abstract: 

    The vasopressin V2 receptor (V2R), a class A G protein-coupled receptor, is essential for regulating body water homeostasis. V2R antagonists have emerged as promising treatments for hyponatremia; however, the absence of structural information for antagonist-bound V2R hampers our understanding of antagonist recognition and the targeted design of V2R antagonists. In this study, we present two cryo-electron microscopy structures of inactive V2R bound to the clinically approved antagonists tolvaptan and conivaptan. Combined with functional analyses and molecular dynamic simulations, these structures reveal distinct binding poses: tolvaptan is deeply inserted within the binding pocket, whereas conivaptan is positioned at a shallower depth. Integrated analyses further define critical pharmacophoric features governing antagonist activity and unveil a TM7 helical conformation-dependent antagonism mechanism that is distinct from classical GPCR inactivation modes. Our findings deepen understanding of antagonist recognition and antagonism of V2R, providing a foundation for the development of V2R-targeted therapies.


  • Organizational Affiliation
    • Lingang Laboratory, Shanghai, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
anti-BRIL Fab heavy chainA [auth H]229Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
anti-BRIL Fab light chainB [auth L]216Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Vasopressin V2 receptor,Soluble cytochrome b562C [auth R]460Homo sapiensEscherichia coliMutation(s): 0 
Gene Names: AVPR2ADHRDIRDIR3V2RcybC
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 P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7P30518
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ECE (Subject of Investigation/LOI)
Query on A1ECE

Download Ideal Coordinates CCD File 
D [auth R]Conivaptan
C32 H26 N4 O2
IKENVDNFQMCRTR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release