6HIS

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

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 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. 


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:  
    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 ...

    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. hugues.nury@ibs.fr.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5-hydroxytryptamine receptor 3AA,
C [auth B],
D [auth C],
E [auth D],
B [auth E]		451Mus musculusMutation(s): 0 
Gene Names: Htr3a, 5ht3, Htr3
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
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, H, I, K, L, N, O, Q, R, T
F, H, I, K, L, N, O, Q, R, T
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG, J, M, P, S 3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TKT
Query on TKT
Download Ideal Coordinates CCD File 
U [auth A],
V [auth E],
W [auth B],
X [auth C],
Y [auth D]		(3-ENDO)-8-METHYL-8-AZABICYCLO[3.2.1]OCT-3-YL 1H-INDOLE-3-CARBOXYLATE
C17 H20 N2 O2
ZNRGQMMCGHDTEI-ITGUQSILSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
TKT BindingDB:  6HIS Ki: min: 0.5, max: 4332 (nM) from 20 assay(s)
Kd: min: 0.79, max: 30 (nM) from 3 assay(s)
IC50: min: 1.3, max: 3.1 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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: 2018-11-28
    Changes: Data collection, Database references
  • 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: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary