Biological Assembly 1  

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 268.89 kDa 
• Atom Count: 16,861 
• Modelled Residue Count: 1,965 
• Deposited Residue Count: 2,250 
• Unique protein chains: 1

 6W1J

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

• PDB DOI: 10.2210/pdb6W1J/pdb
• EM Map EMD-21511: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2020-03-04 Released: 2021-01-13 
• Deposition Author(s): Basak, S., Chakrapani, S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

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

Literature

High-resolution structures of multiple 5-HT 3A R-setron complexes reveal a novel mechanism of competitive inhibition.

Basak, S., Kumar, A., Ramsey, S., Gibbs, E., Kapoor, A., Filizola, M., Chakrapani, S.

(2020) Elife 9

• PubMed: 33063666 
• DOI: 10.7554/eLife.57870
• Primary Citation of Related Structures:  
  6W1J, 6W1M, 6W1Y


• PubMed Abstract: 
  

Serotonin receptors (5-HT _3A R) play a crucial role in regulating gut movement, and are the principal target of setrons, a class of high-affinity competitive antagonists, used in the management of nausea and vomiting associated with radiation and chemotherapies. Structural insights into setron-binding poses and their inhibitory mechanisms are just beginning to emerge. Here, we present high-resolution cryo-EM structures of full-length 5-HT _3A R in complex with palonosetron, ondansetron, and alosetron. Molecular dynamic simulations of these structures embedded in a fully-hydrated lipid environment assessed the stability of ligand-binding poses and drug-target interactions over time. Together with simulation results of apo- and serotonin-bound 5-HT _3A R, the study reveals a distinct interaction fingerprint between the various setrons and binding-pocket residues that may underlie their diverse affinities. In addition, varying degrees of conformational change in the setron-5-HT _3A R structures, throughout the channel and particularly along the channel activation pathway, suggests a novel mechanism of competitive inhibition.

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Related Citations: 

• Molecular mechanism of setron-mediated inhibition of full-length 5-HT3A receptor
  Filizola, M., Basak, S., Gicheru, Y., Kapoor, A., Mayer, M., Chakrapani, S.
  (2019) Nat Commun 10: 3225

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Organizational Affiliation: 

Department of Neuroscience, School of Medicine, Case Western Reserve University, Cleveland, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-hydroxytryptamine receptor 3A	A, B, C, D, E	450	Mus musculus	Mutation(s): 0  Gene Names: Htr3a, 5ht3, Htr3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P23979 (Mus musculus) Explore P23979  Go to UniProtKB:  P23979
IMPC:  MGI:96282

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(4-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, I, L, O, R	2	N/A	N-Glycosylation

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, J, M, P, S	3	N/A	N-Glycosylation

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, K, N, Q, T	2	N/A	N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S7Y (Subject of Investigation/LOI)	U [auth A], V [auth B], W [auth C], X [auth D], Z [auth E]	alosetron C17 H18 N4 O JSWZEAMFRNKZNL-UHFFFAOYSA-N
CL	Y [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX	1.13-2998

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-01-13 
Deposition Author(s): Basak, S., Chakrapani, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM108921
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	3R01GM108921-03S1

Revision History  

• Version 1.0: 2021-01-13
  Type: Initial release