8BL8 | pdb_00008bl8

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

(2024) Nat Struct Mol Biol 31: 1232-1242

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 ₃R), which features two properties: VTX acts differently on rodent and human 5-HT ₃R, 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 ₃R and an agonist-bound-like state of human 5-HT ₃R, in line with the functional profile of the drug. We report four human 5-HT ₃R 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

Macromolecule Content

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-hydroxytryptamine receptor 3A	A, B, C, D, E	397	Homo sapiens	Mutation(s): 0 Gene Names: HTR3A, 5HT3R, HTR3 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46098
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E	Go to GlyGen: P46098-1
Sequence Annotations Expand
Reference Sequence

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, G, H, I, J F, G, H, I, J, K, L, M, N, O	2		N-Glycosylation	Interactions Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Interactions & Density Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth C] SDF format, chain T [auth E] SDF format, chain S [auth D] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth C] MOL2 format, chain T [auth E] MOL2 format, chain S [auth D] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth C] mmCIF format, chain T [auth E] mmCIF format, chain S [auth D]	P [auth A], Q [auth B], R [auth C], S [auth D], T [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth E] Interactions & Density Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth E]