Human serotonin 5-HT3A receptor (apo, active/distorted conformation)

Experimental Data Snapshot

  • Resolution: 3.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

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Structural determinants for activity of the antidepressant vortioxetine at human and rodent 5-HT 3 receptors.

Lopez-Sanchez, U.Munro, L.J.Ladefoged, L.K.Pedersen, A.J.Brun, C.C.Lyngby, S.M.Baud, D.Juillan-Binard, C.Pedersen, M.G.Lummis, S.C.R.Bang-Andersen, B.Schiott, B.Chipot, C.Schoehn, G.Neyton, J.Dehez, F.Nury, H.Kristensen, A.S.

(2024) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-024-01282-x
  • Primary Citation of Related Structures:  
    8AW2, 8AXD, 8BL8, 8BLA, 8BLB

  • PubMed Abstract: 

    Vortioxetine (VTX) is a recently approved antidepressant that targets a variety of serotonin receptors. Here, we investigate the drug's molecular mechanism of operation at the serotonin 5-HT 3 receptor (5-HT 3 R), which features two properties: VTX acts differently on rodent and human 5-HT 3 R, and VTX appears to suppress any subsequent response to agonists. Using a combination of cryo-EM, electrophysiology, voltage-clamp fluorometry and molecular dynamics, we show that VTX stabilizes a resting inhibited state of the mouse 5-HT 3 R and an agonist-bound-like state of human 5-HT 3 R, in line with the functional profile of the drug. We report four human 5-HT 3 R structures and show that the human receptor transmembrane domain is intrinsically fragile. We also explain the lack of recovery after VTX administration via a membrane partition mechanism.

  • Organizational Affiliation

    University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5-hydroxytryptamine receptor 3A
A, B, C, D, E
397Homo sapiensMutation(s): 0 
Gene Names: HTR3A5HT3RHTR3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P46098 (Homo sapiens)
Explore P46098 
Go to UniProtKB:  P46098
PHAROS:  P46098
GTEx:  ENSG00000166736 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46098
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
F, G, H, I, J
F, G, H, I, J, K, L, M, N, O
Experimental Data & Validation

Experimental Data

  • Resolution: 3.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union637733

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release