6NP0

Cryo-EM structure of 5HT3A receptor in presence of granisetron


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular mechanism of setron-mediated inhibition of full-length 5-HT3Areceptor.

Basak, S.Gicheru, Y.Kapoor, A.Mayer, M.L.Filizola, M.Chakrapani, S.

(2019) Nat Commun 10: 3225-3225

  • DOI: 10.1038/s41467-019-11142-8

  • PubMed Abstract: 
  • Serotonin receptor (5-HT <sub>3A </sub>R) is the most common therapeutic target to manage the nausea and vomiting during cancer therapies and in the treatment of irritable bowel syndrome. Setrons, a class of competitive antagonists, cause functional ...

    Serotonin receptor (5-HT 3A R) is the most common therapeutic target to manage the nausea and vomiting during cancer therapies and in the treatment of irritable bowel syndrome. Setrons, a class of competitive antagonists, cause functional inhibition of 5-HT 3A R in the gastrointestinal tract and brainstem, acting as effective anti-emetic agents. Despite their prevalent use, the molecular mechanisms underlying setron binding and inhibition of 5-HT 3A R are not fully understood. Here, we present the structure of granisetron-bound full-length 5-HT 3A R solved by single-particle cryo-electron microscopy to 2.92 Å resolution. The reconstruction reveals the orientation of granisetron in the orthosteric site with unambiguous density for interacting sidechains. Molecular dynamics simulations and electrophysiology confirm the granisetron binding orientation and the residues central for ligand recognition. Comparison of granisetron-bound 5-HT 3A R with the apo and serotonin-bound structures, reveals key insights into the mechanism underlying 5-HT 3A R inhibition.


    Organizational Affiliation

    Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA.,Department of Neuroscience, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106-4970, USA. Sudha.chakrapani@case.edu.,Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA.,Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA. Sudha.chakrapani@case.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5-hydroxytryptamine receptor 3A
A, B, C, D, E
489Mus musculusMutation(s): 0 
Gene Names: Htr3a (5ht3, Htr3)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Cys-Loop Receptor Family
Protein: 
Serotonin 5-HT3A receptor
Find proteins for P23979 (Mus musculus)
Go to UniProtKB:  P23979
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
BMA
Query on BMA

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

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Download CCD File 
A, B, C, D
1-methyl-N-[(1R,5S)-9-methyl-9-azabicyclo[3.3.1]nonan-3-yl]indazole-3-carboxamide
GRANISETRON
C18 H24 N4 O
MFWNKCLOYSRHCJ-BTTYYORXSA-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: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States1R01GM108921
National Institutes of Health/National Institute of General Medical SciencesUnited States3R01GM108921-03S1
American Heart AssociationUnited States17POST33671152

Revision History 

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-07-31
    Type: Data collection, Database references