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Structure of a potentially open state of a proton-activated pentameric ligand-gated ion channel

Abstract

The X-ray structure of a pentameric ligand-gated ion channel from Erwinia chrysanthemi (ELIC) has recently provided structural insight into this family of ion channels at high resolution1. The structure shows a homo-pentameric protein with a barrel-stave architecture that defines an ion-conduction pore located on the fivefold axis of symmetry. In this structure, the wide aqueous vestibule that is encircled by the extracellular ligand-binding domains of the five subunits narrows to a discontinuous pore that spans the lipid bilayer. The pore is constricted by bulky hydrophobic residues towards the extracellular side, which probably serve as barriers that prevent the diffusion of ions. This interrupted pore architecture in ELIC thus depicts a non-conducting conformation of a pentameric ligand-gated ion channel, the thermodynamically stable state in the absence of bound ligand. As ligand binding promotes pore opening in these ion channels and the specific ligand for ELIC has not yet been identified, we have turned our attention towards a homologous protein from the cyanobacterium Gloebacter violaceus (GLIC). GLIC was shown to form proton-gated channels that are activated by a pH decrease on the extracellular side and that do not desensitize after activation2. Both prokaryotic proteins, ELIC and GLIC form ion channels that are selective for cations over anions with poor discrimination among monovalent cations1,2, characteristics that resemble the conduction properties of the cation-selective branch of the family that includes acetylcholine and serotonin receptors3,4. Here we present the X-ray structure of GLIC at 3.1 Å resolution. The structure reveals a conformation of the channel that is distinct from ELIC and that probably resembles the open state. In combination, both structures suggest a novel gating mechanism for pentameric ligand-gated ion channels where channel opening proceeds by a change in the tilt of the pore-forming helices.

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Figure 1: GLIC structure.
Figure 2: Comparison of the pore region.
Figure 3: Pore structure and ion binding.
Figure 4: Extracellular domain.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Coordinates of GLIC have been deposited in the Protein Data Bank under accession number 3EHZ (WT), and 3EI0 (E221A).

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Acknowledgements

We thank B. Blattmann and C. Stutz-Duocommun for assistance with crystal screening, C. Schulze-Briese and the staff of the X06SA beamline for support during data collection, the protein analysis group at the functional genomics centre of the University of Zurich for help with mass spectrometry, R. MacKinnon for comments on the manuscript and members of the Dutzler laboratory for help in all stages of the project. Data collection was performed at the Swiss Light Source of the Paul Scherrer Institute. The research leading to these results was supported by a grant from the National Center for Competence in Research (NCCR) in Structural Biology and by an EC FP7 grant for the EDICT consortium (HEALTH-201924). R.J.C.H. is affiliated with the Molecular Life Sciences Ph.D. programme of the University/ETH Zurich.

Author Contributions R.D. and R.J.C.H. designed the project. R.J.C.H. carried out all experiments. R.D. assisted in data collection and structure determination. R.D. and R.J.C.H. jointly wrote the manuscript.

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Correspondence to Raimund Dutzler.

Supplementary information

Supplementary Information

This file contains Supplementary Figures S1-S10 with Legends and Supplementary Tables S1 -S2. (PDF 2340 kb)

Supplementary Movie 1

Supplementary Movie 1 contains a morph of conserved parts of the Ca trace between ELIC and GLIC. The view is from the extracellular side. (MPG 1711 kb)

Supplementary Movie 2

Supplementary Movie 2 contains a morph of conserved parts of the Ca trace between ELIC and GLIC. The view is from within the membrane. (MPG 1583 kb)

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Hilf, R., Dutzler, R. Structure of a potentially open state of a proton-activated pentameric ligand-gated ion channel. Nature 457, 115–118 (2009). https://doi.org/10.1038/nature07461

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