8FRW | pdb_00008frw

Full-length mouse 5-HT3A receptor in complex with ALB148471, pre-activated


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 8FRW

This is version 1.3 of the entry. See complete history

Literature

Structural basis for partial agonism in 5-HT 3A receptors.

Felt, K.Stauffer, M.Salas-Estrada, L.Guzzo, P.R.Xie, D.Huang, J.Filizola, M.Chakrapani, S.

(2024) Nat Struct Mol Biol 31: 598-609

  • DOI: https://doi.org/10.1038/s41594-023-01140-2
  • Primary Citation Related Structures: 
    8FRW, 8FRX, 8FRZ, 8FSB, 8FSP, 8FSZ

  • PubMed Abstract: 

    Hyperactivity of serotonin 3 receptors (5-HT 3 R) underlies pathologies associated with irritable bowel syndrome and chemotherapy-induced nausea and vomiting. Setrons, a class of high-affinity competitive antagonists, are used in the treatment of these conditions. Although generally effective for chemotherapy-induced nausea and vomiting, the use of setrons for treating irritable bowel syndrome has been impaired by adverse side effects. Partial agonists are now being considered as an alternative strategy, with potentially less severe side effects than full antagonists. However, a structural understanding of how these ligands work is lacking. Here, we present high-resolution cryogenic electron microscopy structures of the mouse 5-HT 3A R in complex with partial agonists (SMP-100 and ALB-148471) captured in pre-activated and open-like conformational states. Molecular dynamics simulations were used to assess the stability of drug-binding poses and interactions with the receptor over time. Together, these studies reveal mechanisms for the functional differences between orthosteric partial agonists, full agonists and antagonists of the 5-HT 3A R.


  • Organizational Affiliation
    • Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA.

Macromolecule Content 

  • Total Structure Weight: 316.62 kDa 
  • Atom Count: 16,680 
  • Modeled Residue Count: 1,975 
  • Deposited Residue Count: 2,765 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
5-hydroxytryptamine receptor 3A
A, B, C, D, E
553Mus 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
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P23979-1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y7H

Query on Y7H



Download:Ideal Coordinates CCD File
I [auth A],
J [auth B],
N [auth C],
R [auth D],
V [auth E]
5-[(1R,3S,5R)-1-azabicyclo[3.2.2]nonan-3-yl]-1,3,4,5-tetrahydro-6H-azepino[5,4,3-cd]indazol-6-one
C18 H22 N4 O
IZPGDYACPJMETA-ZDUSSCGKSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
K [auth B]
L [auth B]
F [auth A],
G [auth A],
H [auth A],
K [auth B],
L [auth B],
M [auth B],
O [auth C],
P [auth C],
Q [auth C],
S [auth D],
T [auth D],
U [auth D],
W [auth E],
X [auth E],
Y [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2-4158

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 StatesGM134896
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM134896-2S1

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Database references
  • Version 1.3: 2024-10-23
    Changes: Data collection, Structure summary