1. Structural Biology and Molecular Biophysics

Structural Insights into Human Acid-sensing Ion Channel 1a Inhibition by Snake Toxin Mambalgin1

  1. Changlin Tian  Is a corresponding author
  2. Demeng Sun
  3. Sanling Liu
  4. Siyu Li
  5. Mengge Zhang
  6. Fan Yang
  7. Ming Wen
  8. Pan Shi
  9. Tao Wang
  10. Man Pan
  11. Shenghai Chang
  12. Xing Zhang
  13. Longhua Zhang
  14. Lei Liu
  1. University of Science and Tehnology of China, China
  2. University of Science and Technology of China, China
  3. Chinese Academy of Sciences, China
  4. Tsinghua University, China
  5. Zhejiang University, China
https://doi.org/10.7554/eLife.57096
Share this article
Cite this article
  1. Changlin Tian
  2. Demeng Sun
  3. Sanling Liu
  4. Siyu Li
  5. Mengge Zhang
  6. Fan Yang
  7. Ming Wen
  8. Pan Shi
  9. Tao Wang
  10. Man Pan
  11. Shenghai Chang
  12. Xing Zhang
  13. Longhua Zhang
  14. Lei Liu
(2020)
Structural Insights into Human Acid-sensing Ion Channel 1a Inhibition by Snake Toxin Mambalgin1
eLife 9:e57096.
https://doi.org/10.7554/eLife.57096
  2. Download BibTeX
  3. Download .RIS

Abstract

Acid-sensing ion channels (ASICs) are proton-gated cation channels that are involved in diverse neuronal processes including pain sensing. Peptide toxin Mambalgin1 (Mamba1) from black mamba snake venom can reversibly inhibit the conductance of ASICs, showing an analgesic effect. However, the detailed inhibitory mechanism of Mamba1 on ASIC1s, especially how Mamba1 binding to extracellular domain affects the conformational changes of the transmembrane domain of ASICs remains elusive. Here, we present single-particle cryo-EM structures of human ASIC1a (hASIC1a) and hASIC1a-Mamba1 complex at resolutions of 3.56 and 3.90 Å, respectively. The structures revealed the inhibited conformation of hASIC1a upon Mamba1 binding. The combination of the structural and physiological data indicates that Mamba1 prefers to bind hASIC1a in a closed state and reduces the proton sensitivity of the channel, representing a closed-state trapping mechanism.

Data availability

The EM maps for hASIC1a and hASIC1a-Mamba1 complex have been deposited in EMDB (www.ebi.ac.uk/pdbe/emdb/) with accession codes EMD-30346 and EMD-30347. The atomic coordinates for hASIC1a and hASIC1a-Mamba1 complex have been deposited in the Protein Data Bank (www.rcsb.org) with accession codes 7CFS and 7CFT respectively

The following previously published data sets were used

Article and author information

Author details

  1. Changlin Tian

    School of Life Science, University of Science and Tehnology of China, Hefei, China
    For correspondence
    cltian@ustc.edu.cn
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9315-900X

  2. Demeng Sun

    School of Life Sciences, University of Science and Technology of China, Hefei, China
    Competing interests
    The authors declare that no competing interests exist.

  3. Sanling Liu

    School of Life Science, University of Science and Tehnology of China, Hefei, China
    Competing interests
    The authors declare that no competing interests exist.

  4. Siyu Li

    School of Life Science, University of Science and Tehnology of China, Hefei, China
    Competing interests
    The authors declare that no competing interests exist.

  5. Mengge Zhang

    School of Life Science, University of Science and Tehnology of China, Hefei, China
    Competing interests
    The authors declare that no competing interests exist.

  6. Fan Yang

    School of Life Science, University of Science and Tehnology of China, Hefei, China
    Competing interests
    The authors declare that no competing interests exist.

  7. Ming Wen

    School of Life Science, University of Science and Tehnology of China, Hefei, China
    Competing interests
    The authors declare that no competing interests exist.

  8. Pan Shi

    School of Life Science, University of Science and Tehnology of China, Hefei, China
    Competing interests
    The authors declare that no competing interests exist.

  9. Tao Wang

    High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, China
    Competing interests
    The authors declare that no competing interests exist.

  10. Man Pan

    Department of Chemistry, Tsinghua University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.

  11. Shenghai Chang

    School of Medicine, Zhejiang University, Hangzhou, China
    Competing interests
    The authors declare that no competing interests exist.

  12. Xing Zhang

    School of Medicine, Zhejiang University, Hangzhou, China
    Competing interests
    The authors declare that no competing interests exist.

  13. Longhua Zhang

    School of Life Science, University of Science and Tehnology of China, Hefei, China
    Competing interests
    The authors declare that no competing interests exist.

  14. Lei Liu

    Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.

Funding

Ministry of Science and Technology of the People's Republic of China (National Key Research and Development Project,2017YFA0505201,2017YFA0505403 and 2016YFA0400903)

  • Changlin Tian

Chinese Academy of Sciences (Queensland-Chinese Academy of Sciences (Q-CAS) Collaborative Science Fund,GJHZ201946)

  • Changlin Tian

Ministry of Science and Technology of the People's Republic of China (National Key Research and Development Project,2017YFA0505200)

  • Lei Liu

National Natural Science Foundation of China (31600601,21778051)

  • Demeng Sun

National Natural Science Foundation of China (91753205,21532004)

  • Lei Liu

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

Reviewing Editor

  1. Leon D Islas, Universidad Nacional Autónoma de México, Mexico

Version history

  1. Received: March 20, 2020
  2. Accepted: September 10, 2020
  3. Accepted Manuscript published: September 11, 2020 (version 1)
  4. Version of Record published: October 13, 2020 (version 2)

Copyright

© 2020, Tian 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

  • 3,263
    Page views
  • 606
    Downloads
  • 24
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

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. Changlin Tian
  2. Demeng Sun
  3. Sanling Liu
  4. Siyu Li
  5. Mengge Zhang
  6. Fan Yang
  7. Ming Wen
  8. Pan Shi
  9. Tao Wang
  10. Man Pan
  11. Shenghai Chang
  12. Xing Zhang
  13. Longhua Zhang
  14. Lei Liu
(2020)
Structural Insights into Human Acid-sensing Ion Channel 1a Inhibition by Snake Toxin Mambalgin1
eLife 9:e57096.
https://doi.org/10.7554/eLife.57096

Categories and tags

Research organism

Further reading

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    The neuronal calcium sensor NCS-1 regulates the phosphorylation state and activity of the Ga chaperone and GEF Ric-8A

    Daniel Muñoz-Reyes, Levi J McClelland ... Maria Jose Sanchez-Barrena
    Research Article

    The Neuronal Calcium Sensor 1, an EF-hand Ca2+ binding protein, and Ric-8A coregulate synapse number and probability of neurotransmitter release. Recently, the structures of Ric-8A bound to Ga have revealed how Ric-8A phosphorylation promotes Ga recognition and activity as a chaperone and guanine nucleotide exchange factor. However, the molecular mechanism by which NCS-1 regulates Ric-8A activity and its interaction with Ga subunits is not well understood. Given the interest in the NCS-1/Ric-8A complex as a therapeutic target in nervous system disorders, it is necessary to shed light on this molecular mechanism of action at atomic level. We have reconstituted NCS-1/Ric-8A complexes to conduct a multimodal approach and determine the sequence of Ca2+ signals and phosphorylation events that promote the interaction of Ric-8A with Ga. Our data show that the binding of NCS-1 and Ga to Ric-8A are mutually exclusive. Importantly, NCS-1 induces a structural rearrangement in Ric-8A that traps the protein in a conformational state that is inaccessible to Casein Kinase II-mediated phosphorylation, demonstrating one aspect of its negative regulation of Ric-8A-mediated G-protein signaling. Functional experiments indicate a loss of Ric-8A GEF activity towards Ga when complexed with NCS-1, and restoration of nucleotide exchange activity upon increasing Ca2+ concentration. Finally, the high-resolution crystallographic data reported here define the NCS-1/Ric-8A interface and will allow the development of therapeutic synapse function regulators with improved activity and selectivity.

    1. Cell Biology
    2. Structural Biology and Molecular Biophysics

    Baited reconstruction with 2D template matching for high-resolution structure determination in vitro and in vivo without template bias

    Bronwyn A Lucas, Benjamin A Himes, Nikolaus Grigorieff
    Research Advance

    Previously we showed that 2D template matching (2DTM) can be used to localize macromolecular complexes in images recorded by cryogenic electron microscopy (cryo-EM) with high precision, even in the presence of noise and cellular background (Lucas et al., 2021; Lucas et al., 2022). Here, we show that once localized, these particles may be averaged together to generate high-resolution 3D reconstructions. However, regions included in the template may suffer from template bias, leading to inflated resolution estimates and making the interpretation of high-resolution features unreliable. We evaluate conditions that minimize template bias while retaining the benefits of high-precision localization, and we show that molecular features not present in the template can be reconstructed at high resolution from targets found by 2DTM, extending prior work at low-resolution. Moreover, we present a quantitative metric for template bias to aid the interpretation of 3D reconstructions calculated with particles localized using high-resolution templates and fine angular sampling.

    1. Plant Biology
    2. Structural Biology and Molecular Biophysics

    Vicia faba SV channel VfTPC1 is a hyperexcitable variant of plant vacuole Two Pore Channels

    Jinping Lu, Ingo Dreyer ... Rainer Hedrich
    Research Article

    To fire action-potential-like electrical signals, the vacuole membrane requires the two-pore channel TPC1, formerly called SV channel. The TPC1/SV channel functions as a depolarization-stimulated, non-selective cation channel that is inhibited by luminal Ca2+. In our search for species-dependent functional TPC1 channel variants with different luminal Ca2+ sensitivity, we found in total three acidic residues present in Ca2+ sensor sites 2 and 3 of the Ca2+-sensitive AtTPC1 channel from Arabidopsis thaliana that were neutral in its Vicia faba ortholog and also in those of many other Fabaceae. When expressed in the Arabidopsis AtTPC1-loss-of-function background, wild-type VfTPC1 was hypersensitive to vacuole depolarization and only weakly sensitive to blocking luminal Ca2+. When AtTPC1 was mutated for these VfTPC1-homologous polymorphic residues, two neutral substitutions in Ca2+ sensor site 3 alone were already sufficient for the Arabidopsis At-VfTPC1 channel mutant to gain VfTPC1-like voltage and luminal Ca2+ sensitivity that together rendered vacuoles hyperexcitable. Thus, natural TPC1 channel variants exist in plant families which may fine-tune vacuole excitability and adapt it to environmental settings of the particular ecological niche.