Dynamic closed states of a ligand-gated ion channel captured by cryo-EM and simulations

Life Sci Alliance. 2021 Jul 1;4(8):e202101011. doi: 10.26508/lsa.202101011. Print 2021 Aug.


Ligand-gated ion channels are critical mediators of electrochemical signal transduction across evolution. Biophysical and pharmacological characterization of these receptor proteins relies on high-quality structures in multiple, subtly distinct functional states. However, structural data in this family remain limited, particularly for resting and intermediate states on the activation pathway. Here, we report cryo-electron microscopy (cryo-EM) structures of the proton-activated Gloeobacter violaceus ligand-gated ion channel (GLIC) under three pH conditions. Decreased pH was associated with improved resolution and side chain rearrangements at the subunit/domain interface, particularly involving functionally important residues in the β1-β2 and M2-M3 loops. Molecular dynamics simulations substantiated flexibility in the closed-channel extracellular domains relative to the transmembrane ones and supported electrostatic remodeling around E35 and E243 in proton-induced gating. Exploration of secondary cryo-EM classes further indicated a low-pH population with an expanded pore. These results allow us to define distinct protonation and activation steps in pH-stimulated conformational cycling in GLIC, including interfacial rearrangements largely conserved in the pentameric channel family.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry
  • Cryoelectron Microscopy
  • Cyanobacteria / chemistry
  • Cyanobacteria / metabolism*
  • Hydrogen-Ion Concentration
  • Ligand-Gated Ion Channels / chemistry*
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Protein Conformation
  • Protein Domains


  • Bacterial Proteins
  • Ligand-Gated Ion Channels

Supplementary concepts

  • Gloeobacter violaceus

Associated data

  • PDB/4NPQ
  • PDB/4HFI
  • PDB/6ZGD
  • PDB/6ZGJ
  • PDB/6ZGK