8C20 | pdb_00008c20

Tetrameric 5-HT3aR in Salipro (holo state, symmetric)

• PDB DOI: https://doi.org/10.2210/pdb8C20/pdb
• EM Map EMD-16386: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMmpstruc


• Deposited: 2022-12-21 Released: 2024-07-10 
• Deposition Author(s): Introini, B., Kudryashev, M.
• Funding Organization(s): Alexander von Humboldt Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of tetrameric forms of the serotonin-gated 5-HT3 A receptor ion channel.

Introini, B., Cui, W., Chu, X., Zhang, Y., Alves, A.C., Eckhardt-Strelau, L., Golusik, S., Tol, M., Vogel, H., Yuan, S., Kudryashev, M.

(2024) EMBO J 43: 4451-4471

• PubMed: 39232129 
• DOI: https://doi.org/10.1038/s44318-024-00191-5
• Primary Citation of Related Structures:  
  8C1W, 8C1Z, 8C20, 8C21


• PubMed Abstract: 
  

  Multimeric membrane proteins are produced in the endoplasmic reticulum and transported to their target membranes which, for ion channels, is typically the plasma membrane. Despite the availability of many fully assembled channel structures, our understanding of assembly intermediates, multimer assembly mechanisms, and potential functions of non-standard assemblies is limited. We demonstrate that the pentameric ligand-gated serotonin 5-HT3A receptor (5-HT3AR) can assemble to tetrameric forms and report the structures of the tetramers in plasma membranes of cell-derived microvesicles and in membrane memetics using cryo-electron microscopy and tomography. The tetrameric structures have near-symmetric transmembrane domains, and asymmetric extracellular domains, and can bind serotonin molecules. Computer simulations, based on our cryo-EM structures, were used to decipher the assembly pathway of pentameric 5-HT3R and suggest a potential functional role for the tetrameric receptors.

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Organizational Affiliation: 
• Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University of Frankfurt am Main, Frankfurt on Main, Germany.
The Research Center for Computer-aided Drug Discovery, Institute of Biomedicine and Biotechnology, The Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), In Situ Structural Biology, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
The Research Center for Computer-aided Drug Discovery, Institute of Biomedicine and Biotechnology, The Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China. [e-mail].
Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland. [e-mail].
Faculty of Pharmaceutical Sciences, Shenzhen University of Advanced Technology (SUAT), Shenzhen, China. [e-mail].
The Research Center for Computer-aided Drug Discovery, Institute of Biomedicine and Biotechnology, The Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China. [e-mail].
AlphaMol Science Ltd, Shenzhen, 518055, China. [e-mail].
Max Planck Institute of Biophysics, Frankfurt am Main, Germany. [e-mail].
Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University of Frankfurt am Main, Frankfurt on Main, Germany. [e-mail].
Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), In Situ Structural Biology, Robert-Rössle-Str. 10, 13125, Berlin, Germany. [e-mail].
Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin, Berlin, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy, native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 243.02 kDa 
• Atom Count: 11,701 
• Modeled Residue Count: 1,408 
• Deposited Residue Count: 2,152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-hydroxytryptamine receptor 3A	A, B, C, D	538	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SRO (Subject of Investigation/LOI)	E [auth B], F [auth D]	SEROTONIN C10 H12 N2 O QZAYGJVTTNCVMB-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SRO	BindingDB:  8C20	Ki: min: 66, max: 390 (nM) from 8 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: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Introini, B., Kudryashev, M.

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Funding Organization	Location	Grant Number
Alexander von Humboldt Foundation	Germany	Sofja Kovalevskaja Award to MK

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Structure summary
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references