Mouse serotonin 5-HT3 receptor, serotonin-bound, I1 conformation

Experimental Data Snapshot

  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

This is version 3.0 of the entry. See complete history


Conformational transitions of the serotonin 5-HT3receptor.

Polovinkin, L.Hassaine, G.Perot, J.Neumann, E.Jensen, A.A.Lefebvre, S.N.Corringer, P.J.Neyton, J.Chipot, C.Dehez, F.Schoehn, G.Nury, H.

(2018) Nature 563: 275-279

  • DOI: https://doi.org/10.1038/s41586-018-0672-3
  • Primary Citation of Related Structures:  
    6HIN, 6HIO, 6HIQ, 6HIS

  • PubMed Abstract: 

    The serotonin 5-HT 3 receptor is a pentameric ligand-gated ion channel (pLGIC). It belongs to a large family of receptors that function as allosteric signal transducers across the plasma membrane 1,2 ; upon binding of neurotransmitter molecules to extracellular sites, the receptors undergo complex conformational transitions that result in transient opening of a pore permeable to ions. 5-HT 3 receptors are therapeutic targets for emesis and nausea, irritable bowel syndrome and depression 3 . In spite of several reported pLGIC structures 4-8 , no clear unifying view has emerged on the conformational transitions involved in channel gating. Here we report four cryo-electron microscopy structures of the full-length mouse 5-HT 3 receptor in complex with the anti-emetic drug tropisetron, with serotonin, and with serotonin and a positive allosteric modulator, at resolutions ranging from 3.2 Å to 4.5 Å. The tropisetron-bound structure resembles those obtained with an inhibitory nanobody 5 or without ligand 9 . The other structures include an 'open' state and two ligand-bound states. We present computational insights into the dynamics of the structures, their pore hydration and free-energy profiles, and characterize movements at the gate level and cation accessibility in the pore. Together, these data deepen our understanding of the gating mechanism of pLGICs and capture ligand binding in unprecedented detail.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5-hydroxytryptamine receptor 3AA,
B [auth E],
C [auth B],
D [auth C],
E [auth D]
452Mus 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
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
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
P [auth A],
S [auth E],
T [auth B],
V [auth C],
Y [auth D]
C8 H15 N O6
Query on SRO

Download Ideal Coordinates CCD File 
Q [auth A],
R [auth E],
U [auth B],
W [auth C],
X [auth D]
C10 H12 N2 O
Binding Affinity Annotations 
IDSourceBinding Affinity
SRO BindingDB:  6HIO Ki: min: 66, max: 1.00e+4 (nM) from 10 assay(s)
IC50: 727 (nM) from 1 assay(s)
EC50: min: 141, max: 1.20e+4 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-11-21
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-03
    Changes: Data collection, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.0: 2022-09-14
    Changes: Atomic model, Data collection, Database references, Source and taxonomy, Structure summary