Full-length 5-HT3A receptor in a serotonin-bound conformation- State 2

Experimental Data Snapshot

  • Resolution: 3.89 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


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: https://doi.org/10.1038/s41586-018-0660-7
  • Primary Citation of Related Structures:  
    6DG7, 6DG8

  • 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. 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 Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5-hydroxytryptamine receptor 3A
A, B, C, D, E
455Mus musculusMutation(s): 0 
Gene Names: Htr3a
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, H, J, K, M
F, H, J, K, M, N, P, Q, S, T
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
G, I, L, O, R
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
SRO BindingDB:  6DG8 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: 3.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

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