8AW2

Mouse serotonin 5-HT3A receptor in complex with vortioxetine


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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 31: 1232-1242

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5-hydroxytryptamine receptor 3A
A, B, C, D, E
566Mus musculusMutation(s): 0 
Gene Names: Htr3a5ht3Htr3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P23979 (Mus musculus)
Explore P23979 
Go to UniProtKB:  P23979
IMPC:  MGI:96282
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23979
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P23979-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, H, J, L, N
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, I, K, M, O
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VTX (Subject of Investigation/LOI)
Query on VTX

Download Ideal Coordinates CCD File 
AA [auth D],
DA [auth E],
R [auth A],
U [auth B],
X [auth C]
Vortioxetine
C18 H22 N2 S
YQNWZWMKLDQSAC-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
BA [auth E],
P [auth A],
S [auth B],
V [auth C],
Y [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
CA [auth E],
Q [auth A],
T [auth B],
W [auth C],
Z [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
VTX BindingDB:  8AW2 Ki: 230 (nM) from 1 assay(s)
IC50: 0.18 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv3.3.1
MODEL REFINEMENTPHENIX1.20

Structure Validation

View Full Validation Report



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: 2024-03-06
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Database references
  • Version 1.2: 2024-08-28
    Changes: Data collection, Database references
  • Version 1.3: 2024-10-16
    Changes: Data collection, Structure summary