9HB3 | pdb_00009hb3

cryo-EM structure of inactive human arginine-vasopressin (AVP) V2 receptor (V2R) with Mambaquaretin1 K39A (MQK39A)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Inactive structures of the vasopressin V2 receptor reveal distinct binding modes for Tolvaptan and Mambaquaretin toxin.

Fouillen, A.Bous, J.Couvineau, P.Orcel, H.Mary, C.Lafleur, L.Pierre, T.Mendre, C.Gilles, N.Schulte, G.Granier, S.Mouillac, B.

(2025) Nat Commun 16: 3899-3899

  • DOI: https://doi.org/10.1038/s41467-025-59114-5
  • Primary Citation of Related Structures:  
    9HAP, 9HB3

  • PubMed Abstract: 

    Inhibitors of the arginine-vasopressin (AVP) V2 receptor (V2R) are key therapeutic compounds for treating hyponatremia or polycystic kidney diseases. Rational drug design based on experimental G protein-coupled receptor structures is a powerful avenue to develop better drugs. So far, the lack of inhibitor-bound V2R structures has impaired this strategy. Here we describe the cryo-electron microscopy structures of the V2R in complex with two selective inverse agonists, the non-peptide Tolvaptan (TVP) and the green mamba snake Mambaquaretin toxin (MQ1). Both ligands bind into the orthosteric binding site but with substantial differences. TVP binds deeper than MQ1, and directly contacts the toggle switch residue W284 6.48 in the transmembrane domain 6. The Kunitz-fold toxin displays extensive contacts with extracellular and transmembrane residues. As anticipated from TVP and MQ1 pharmacological properties, both structures represent inactive V2R conformations. Their comparison with those of the active AVP-bound V2R reveals the molecular mechanisms modulating receptor activity. The mini-protein MQ1-bound V2R structure suggests a new pharmacology approach for treating water homeostasis and renal diseases.


  • Organizational Affiliation
    • Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier cedex 5, France.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mambaquaretin-157Dendroaspis angusticepsMutation(s): 1 
UniProt
Find proteins for A0A1Z0YU59 (Dendroaspis angusticeps)
Explore A0A1Z0YU59 
Go to UniProtKB:  A0A1Z0YU59
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UniProt GroupA0A1Z0YU59
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Synthetic antibody, anti-BRIL Fab fragment, Heavy chainB [auth H]231Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
anti-BRIL Fab NanobodyC [auth K]141Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Synthetic antibody, anti-BRIL Fab fragment, Light chainD [auth L]215Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
arginine-vasopressin (AVP) V2 receptor (V2R)-BRIL,Vasopressin V2 receptor,Vasopressin V2 receptorE [auth R]552Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P30518 (Homo sapiens)
Explore P30518 
Go to UniProtKB:  P30518
PHAROS:  P30518
GTEx:  ENSG00000126895 
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UniProt GroupP30518
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRosetta
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4.5.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-19-CE11-0014
Agence Nationale de la Recherche (ANR)FranceANR-22-CE44-0021
H2020 Marie Curie Actions of the European CommissionEuropean Union101063049_3D-V2R

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release