6DG7

Full-length 5-HT3A receptor in a serotonin-bound conformation- State 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Cryo-EM reveals two distinct serotonin-bound conformations of full-length 5-HT3Areceptor.

Basak, S.Gicheru, Y.Rao, S.Sansom, M.S.P.Chakrapani, S.

(2018) Nature 563: 270-274

  • DOI: 10.1038/s41586-018-0660-7
  • Primary Citation of Related Structures:  
    6DG8, 6DG7

  • PubMed Abstract: 
  • The 5-HT 3A serotonin receptor 1 , a cationic pentameric ligand-gated ion channel (pLGIC), is the clinical target for management of nausea and vomiting associated with radiation and chemotherapies 2 . Upon binding, serotonin induces a global conformational change that encompasses the ligand-binding extracellular domain (ECD), the transmembrane domain (TMD) and the intracellular domain (ICD), the molecular details of which are unclear ...

    The 5-HT 3A serotonin receptor 1 , a cationic pentameric ligand-gated ion channel (pLGIC), is the clinical target for management of nausea and vomiting associated with radiation and chemotherapies 2 . Upon binding, serotonin induces a global conformational change that encompasses the ligand-binding extracellular domain (ECD), the transmembrane domain (TMD) and the intracellular domain (ICD), the molecular details of which are unclear. Here we present two serotonin-bound structures of the full-length 5-HT 3A receptor in distinct conformations at 3.32 Å and 3.89 Å resolution that reveal the mechanism underlying channel activation. In comparison to the apo 5-HT 3A receptor, serotonin-bound states underwent a large twisting motion in the ECD and TMD, leading to the opening of a 165 Å permeation pathway. Notably, this motion results in the creation of lateral portals for ion permeation at the interface of the TMD and ICD. Combined with molecular dynamics simulations, these structures provide novel insights into conformational coupling across domains and functional modulation.


    Organizational Affiliation

    Department of Neuroscience, School of Medicine, Case Western Reserve University, Cleveland, OH, USA. sudha.chakrapani@case.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5-hydroxytryptamine receptor 3AA, B, C, D, E455Mus 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
Oligosaccharides

Help

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, J, K, M, N, P, Q
F, H, J, K, M, N, P, Q, S, 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, I, L, O, R3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
SRO BindingDB:  6DG7 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

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM108921
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States3R01GM108921-03S1
American Heart AssociationUnited States17POST33671152

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: 2020-01-08
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary