6HIS

Mouse serotonin 5-HT3 receptor, tropisetron-bound, T conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1038/s41586-018-0672-3
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The serotonin 5-HT <sub>3 </sub> 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 <sup>1,2 </sup>; upon binding of neurotran ...

    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

    Channel Receptors Unit, CNRS UMR 3571, Institut Pasteur, Paris, France.,CNRS, Université Grenoble Alpes, CEA, IBS, Grenoble, France.,CNRS, Université Grenoble Alpes, CEA, IBS, Grenoble, France. jacques.neyton@ibs.fr.,Université de Lorraine, CNRS, LPCT, Nancy, France.,Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, Vandoeuvre-les-Nancy, France.,CNRS, Université Grenoble Alpes, CEA, IBS, Grenoble, France. hugues.nury@ibs.fr.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Theranyx, Marseille, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5-hydroxytryptamine receptor 3A
A, E, B, C, D
445Mus musculusMutation(s): 0 
Gene Names: Htr3a (5ht3, Htr3)
Find proteins for P23979 (Mus musculus)
Go to UniProtKB:  P23979
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B, C, D, E
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
TKT
Query on TKT

Download SDF File 
Download CCD File 
A, B, C, D, E
(3-ENDO)-8-METHYL-8-AZABICYCLO[3.2.1]OCT-3-YL 1H-INDOLE-3-CARBOXYLATE
TROPISETRON
C17 H20 N2 O2
ZNRGQMMCGHDTEI-ITGUQSILSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-11-21
    Type: Data collection, Database references
  • Version 1.2: 2018-11-28
    Type: Data collection, Database references