Sterol derivative binding to the orthosteric site causes conformational changes in an invertebrate Cys-loop receptor

  1. Steven De Gieter
  2. Casey Gallagher
  3. Eveline Wijckmans
  4. Diletta Pasini
  5. Chris Ulens  Is a corresponding author
  6. Rouslan G Efremov  Is a corresponding author
  1. VIB-VUB Center for Structural Biology, Belgium
  2. KU Leuven, Belgium

Abstract

Cys-loop receptors or pentameric ligand-gated ion channels are mediators of electrochemical signaling throughout the animal kingdom. Because of their critical function in neurotransmission and high potential as drug targets, Cys-loop receptors from humans and closely related organisms have been thoroughly investigated, whereas molecular mechanisms of neurotransmission in invertebrates are less understood. When compared with vertebrates, the invertebrate genomes underwent a drastic expansion in the number of the nACh-like genes associated with receptors of unknown function. Understanding this diversity contributes to better insight into the evolution and possible functional divergence of these receptors. In this work, we studied orphan receptor Alpo4 from an extreme thermophile worm Alvinella pompejana. Sequence analysis points towards its remote relation to characterized nACh receptors. We solved the cryo-EM structure of the lophotrochozoan nACh-like receptor in which a CHAPS molecule is tightly bound to the orthosteric site. We show that the binding of CHAPS leads to extending of the loop C at the orthosteric site and a quaternary twist between extracellular and transmembrane domains. Both the ligand binding site and the channel pore reveal unique features. These include a conserved Trp residue in loop B of the ligand binding site which is flipped into an apparent self-liganded state in the apo structure. The ion pore of Alpo4 is tightly constricted by a ring of methionines near the extracellular entryway of the channel pore. Our data provide a structural basis for a functional understanding of Alpo4 and hints towards new strategies for designing specific channel modulators.

Data availability

The cryo-EM density maps and atomic models generated in this study have been deposited in the PDB and EMDB database under accession codes: 8BYI / EMDB-16326 (Alpo4CHAPS), 8BXF / EMDB- 16317 (Alpo4APO), 8BX5 / EMDB-16308 (Alpo4LMNG_APO), 8BXB / EMDB-16314 (Alpo4ACH), 8BKE / EMDB-16316 (Alpo4COMB), 8BKD / EMDB-16315 (Alpo4SER).

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Steven De Gieter

    VIB-VUB Center for Structural Biology, Brussels, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  2. Casey Gallagher

    Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  3. Eveline Wijckmans

    Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  4. Diletta Pasini

    Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  5. Chris Ulens

    Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
    For correspondence
    chris.ulens@kuleuven.be
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8202-5281
  6. Rouslan G Efremov

    VIB-VUB Center for Structural Biology, Brussels, Belgium
    For correspondence
    rouslan.efremov@vub.vib.be
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7516-8658

Funding

Fonds Wetenschappelijk Onderzoek (G0H5916N)

  • Rouslan G Efremov

Fonds Wetenschappelijk Onderzoek (G054617N)

  • Rouslan G Efremov

Fonds Wetenschappelijk Onderzoek (G0H5916N)

  • Steven De Gieter

Fonds Wetenschappelijk Onderzoek (G0C1319N)

  • Chris Ulens

Fonds Wetenschappelijk Onderzoek (G087921N)

  • Chris Ulens

KU Leuven (C3/19/023)

  • Chris Ulens

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Marcel P Goldschen-Ohm, University of Texas at Austin, United States

Version history

  1. Preprint posted: January 6, 2023 (view preprint)
  2. Received: January 8, 2023
  3. Accepted: July 2, 2023
  4. Accepted Manuscript published: July 3, 2023 (version 1)
  5. Version of Record published: July 12, 2023 (version 2)

Copyright

© 2023, De Gieter et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Steven De Gieter
  2. Casey Gallagher
  3. Eveline Wijckmans
  4. Diletta Pasini
  5. Chris Ulens
  6. Rouslan G Efremov
(2023)
Sterol derivative binding to the orthosteric site causes conformational changes in an invertebrate Cys-loop receptor
eLife 12:e86029.
https://doi.org/10.7554/eLife.86029

Share this article

https://doi.org/10.7554/eLife.86029

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