Cryo-EM structure of the rhodopsin-Gαi-βγ complex reveals binding of the rhodopsin C-terminal tail to the Gβ subunit

Abstract

One of the largest membrane protein families in eukaryotes are G protein-coupled receptors (GPCRs). GPCRs modulate cell physiology by activating diverse intracellular transducers, prominently heterotrimeric G proteins. The recent surge in structural data has expanded our understanding of GPCR-mediated signal transduction. However, many aspects, including the existence of transient interactions, remain elusive. We present the cryo-EM structure of the light-sensitive GPCR rhodopsin in complex with heterotrimeric Gi. Our density map reveals the receptor C-terminal tail bound to the Gβ subunit of the G protein, providing a structural foundation for the role of the C-terminal tail in GPCR signaling, and of Gβ as scaffold for recruiting Gα subunits and G protein-receptor kinases. By comparing available complexes, we found a small set of common anchoring points that are G protein-subtype specific. Taken together, our structure and analysis provide new structural basis for the molecular events of the GPCR signaling pathway.

Data availability

The cryo-EM density map of the rhodopsin-Gi complex bound to Fab16 has been deposited in the EM Data Bank (accession code EMD-4598), and the related structure coordinates have been deposited in the Protein Data Bank (accession code 6QNO). The crystal structure of Fab16 has been deposited in the Protein Data Bank (accession code 6QNK). Source data for Figure 3 is provided in Suppl. Table 3.

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

Article and author information

Author details

  1. Ching-Ju Tsai

    Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8320-5009
  2. Jacopo Marino

    Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7095-0800
  3. Ricardo Adaixo

    Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
    Competing interests
    No competing interests declared.
  4. Filip Pamula

    Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
    Competing interests
    No competing interests declared.
  5. Jonas Muehle

    Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
    Competing interests
    No competing interests declared.
  6. Shoji Maeda

    Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
    Competing interests
    No competing interests declared.
  7. Tilman Flock

    Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3398-0968
  8. Nicholas MI Taylor

    Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0761-4921
  9. Inayatulla Mohammed

    Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
    Competing interests
    No competing interests declared.
  10. Hugues Matile

    Pharma Research and Early Development, Therapeutic modalities, Roche Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland
    Competing interests
    No competing interests declared.
  11. Roger JP Dawson

    Pharma Research and Early Development, Therapeutic modalities, Roche Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland
    Competing interests
    No competing interests declared.
  12. Xavier Deupi

    Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
    For correspondence
    xavier.deupi@psi.ch
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4572-9316
  13. Henning Stahlberg

    Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
    For correspondence
    Henning.Stahlberg@unibas.ch
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1185-4592
  14. Gebhard Schertler

    Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
    For correspondence
    gebhard.schertler@psi.ch
    Competing interests
    Gebhard Schertler, declares that he is a co-founder and scientific advisor of the company leadXpro AG and InterAx Biotech AG, and that he has been a member of the MAX IV Scientific Advisory Committee during the time when the research has been performed..

Funding

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (310030_153145)

  • Gebhard Schertler

Swiss Nanoscience Institute (A13.12 NanoGhip)

  • Gebhard Schertler

National Centres of Competence in Research (TransCure)

  • Henning Stahlberg

Holcim Stiftung

  • Jacopo Marino

ETH Zurich

  • Tilman Flock

University of Cambridge

  • Tilman Flock

Roche

  • Shoji Maeda

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (160805)

  • Xavier Deupi

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (310030B_173335)

  • Gebhard Schertler

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

Copyright

© 2019, Tsai 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.

Metrics

  • 5,212
    views
  • 898
    downloads
  • 59
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Ching-Ju Tsai
  2. Jacopo Marino
  3. Ricardo Adaixo
  4. Filip Pamula
  5. Jonas Muehle
  6. Shoji Maeda
  7. Tilman Flock
  8. Nicholas MI Taylor
  9. Inayatulla Mohammed
  10. Hugues Matile
  11. Roger JP Dawson
  12. Xavier Deupi
  13. Henning Stahlberg
  14. Gebhard Schertler
(2019)
Cryo-EM structure of the rhodopsin-Gαi-βγ complex reveals binding of the rhodopsin C-terminal tail to the Gβ subunit
eLife 8:e46041.
https://doi.org/10.7554/eLife.46041

Share this article

https://doi.org/10.7554/eLife.46041

Further reading

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Angel D'Oliviera, Xuhang Dai ... Jeffrey S Mugridge
    Research Article

    The SARS-CoV-2 main protease (Mpro or Nsp5) is critical for production of viral proteins during infection and, like many viral proteases, also targets host proteins to subvert their cellular functions. Here, we show that the human tRNA methyltransferase TRMT1 is recognized and cleaved by SARS-CoV-2 Mpro. TRMT1 installs the N2,N2-dimethylguanosine (m2,2G) modification on mammalian tRNAs, which promotes cellular protein synthesis and redox homeostasis. We find that Mpro can cleave endogenous TRMT1 in human cell lysate, resulting in removal of the TRMT1 zinc finger domain. Evolutionary analysis shows the TRMT1 cleavage site is highly conserved in mammals, except in Muroidea, where TRMT1 is likely resistant to cleavage. TRMT1 proteolysis results in reduced tRNA binding and elimination of tRNA methyltransferase activity. We also determined the structure of an Mpro-TRMT1 peptide complex that shows how TRMT1 engages the Mpro active site in an uncommon substrate binding conformation. Finally, enzymology and molecular dynamics simulations indicate that kinetic discrimination occurs during a later step of Mpro-mediated proteolysis following substrate binding. Together, these data provide new insights into substrate recognition by SARS-CoV-2 Mpro that could help guide future antiviral therapeutic development and show how proteolysis of TRMT1 during SARS-CoV-2 infection impairs both TRMT1 tRNA binding and tRNA modification activity to disrupt host translation and potentially impact COVID-19 pathogenesis or phenotypes.

    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease
    Qian Wang, Jinxin Liu ... Qian Liu
    Research Article

    Paramyxovirus membrane fusion requires an attachment protein for receptor binding and a fusion protein for membrane fusion triggering. Nipah virus (NiV) attachment protein (G) binds to ephrinB2 or -B3 receptors, and fusion protein (F) mediates membrane fusion. NiV-F is a class I fusion protein and is activated by endosomal cleavage. The crystal structure of a soluble GCN4-decorated NiV-F shows a hexamer-of-trimer assembly. Here, we used single-molecule localization microscopy to quantify the NiV-F distribution and organization on cell and virus-like particle membranes at a nanometer precision. We found that NiV-F on biological membranes forms distinctive clusters that are independent of endosomal cleavage or expression levels. The sequestration of NiV-F into dense clusters favors membrane fusion triggering. The nano-distribution and organization of NiV-F are susceptible to mutations at the hexamer-of-trimer interface, and the putative oligomerization motif on the transmembrane domain. We also show that NiV-F nanoclusters are maintained by NiV-F–AP-2 interactions and the clathrin coat assembly. We propose that the organization of NiV-F into nanoclusters facilitates membrane fusion triggering by a mixed population of NiV-F molecules with varied degrees of cleavage and opportunities for interacting with the NiV-G/receptor complex. These observations provide insights into the in situ organization and activation mechanisms of the NiV fusion machinery.