4PIR

X-ray structure of the mouse serotonin 5-HT3 receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

X-ray structure of the mouse serotonin 5-HT3 receptor.

Hassaine, G.Deluz, C.Grasso, L.Wyss, R.Tol, M.B.Hovius, R.Graff, A.Stahlberg, H.Tomizaki, T.Desmyter, A.Moreau, C.Li, X.D.Poitevin, F.Vogel, H.Nury, H.

(2014) Nature 512: 276-281

  • DOI: 10.1038/nature13552
  • Primary Citation of Related Structures:  
    4PIR

  • PubMed Abstract: 
  • Neurotransmitter-gated ion channels of the Cys-loop receptor family mediate fast neurotransmission throughout the nervous system. The molecular processes of neurotransmitter binding, subsequent opening of the ion channel and ion permeation remain poorly understood ...

    Neurotransmitter-gated ion channels of the Cys-loop receptor family mediate fast neurotransmission throughout the nervous system. The molecular processes of neurotransmitter binding, subsequent opening of the ion channel and ion permeation remain poorly understood. Here we present the X-ray structure of a mammalian Cys-loop receptor, the mouse serotonin 5-HT3 receptor, at 3.5 Å resolution. The structure of the proteolysed receptor, made up of two fragments and comprising part of the intracellular domain, was determined in complex with stabilizing nanobodies. The extracellular domain reveals the detailed anatomy of the neurotransmitter binding site capped by a nanobody. The membrane domain delimits an aqueous pore with a 4.6 Å constriction. In the intracellular domain, a bundle of five intracellular helices creates a closed vestibule where lateral portals are obstructed by loops. This 5-HT3 receptor structure, revealing part of the intracellular domain, expands the structural basis for understanding the operating mechanism of mammalian Cys-loop receptors.


    Organizational Affiliation

    1] Laboratory of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland [2] Université Grenoble Alpes, IBS, F-38000 Grenoble, France [3] CNRS, IBS, F-38000 Grenoble, France [4] CEA, DSV, IBS, F-38000 Grenoble, France.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5-hydroxytryptamine receptor 3AA, B, C, D, E456Mus musculusMutation(s): 0 
Gene Names: Htr3a5ht3Htr3
Membrane Entity: Yes 
UniProt
Find proteins for P23979 (Mus musculus)
Explore P23979 
Go to UniProtKB:  P23979
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
VHH15F, G, H, I, J124Lama glamaMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
K, M, O, P, R, S, U, V
K, M, O, P, R, S, U, V, X
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseL, N, Q, T, W3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.542α = 90
b = 187.087β = 90
c = 240.554γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2014-08-27
    Changes: Database references
  • Version 1.2: 2014-09-17
    Changes: Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary