1. Structural Biology and Molecular Biophysics

Cryo-EM structure of the polycystin 2-l1 ion channel

  1. Raymond E Hulse
  2. Zongli Li
  3. Rick K Huang
  4. Jin Zhang
  5. David E Clapham  Is a corresponding author
  1. Howard Hughes Medical Institute, United States
  2. Harvard Medical School, United States
https://doi.org/10.7554/eLife.36931
Share this article
Cite this article
  1. Raymond E Hulse
  2. Zongli Li
  3. Rick K Huang
  4. Jin Zhang
  5. David E Clapham
(2018)
Cryo-EM structure of the polycystin 2-l1 ion channel
eLife 7:e36931.
https://doi.org/10.7554/eLife.36931
  2. Download BibTeX
  3. Download .RIS

Abstract

We report the near atomic resolution (3.3 Å) of the human polycystic kidney disease 2-like 1 (polycystin 2-l1) ion channel. Encoded by PKD2L1, polycystin 2-l1 is a calcium and monovalent cation-permeant ion channel in primary cilia and plasma membranes. The related primary cilium-specific polycystin-2 protein, encoded by PKD2, shares a high degree of sequence similarity, yet has distinct permeability characteristics. Here we show that these differences are reflected in the architecture of polycystin 2-l1.

Data availability

The cryo map and model have been deposited to the Worldwide Protein Data Bank (6DU8) and Electron Microscopy Data Bank (8912).

The following data sets were generated
    1. Clapham DE
    2. Hulse RE
    3. Li Z
    4. Huang RK
    5. Zhang J
    (2018) Cryo map and model from
    Publicly available at the Worldwide Protein Data Bank (Accession no: 6DU8).
    http://www.wwpdb.org/
    1. Clapham DE
    2. Hulse RE
    3. Li Z
    4. Huang RK
    5. Zhang J
    (2018) Cryo map and model from
    Publicly available at the Electron Microscopy Data Bank (Accession no: 8912).
    https://www.ebi.ac.uk/pdbe/emdb/
The following previously published data sets were used

Article and author information

Author details

  1. Raymond E Hulse

    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0110-3752

  2. Zongli Li

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.

  3. Rick K Huang

    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Jin Zhang

    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    Competing interests
    The authors declare that no competing interests exist.

  5. David E Clapham

    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    For correspondence
    claphamd@hhmi.org
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4459-9428

Funding

Howard Hughes Medical Institute

  • David E Clapham

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

Copyright

© 2018, Hulse 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

  • 2,941
    views
  • 619
    downloads
  • 50
    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. Raymond E Hulse
  2. Zongli Li
  3. Rick K Huang
  4. Jin Zhang
  5. David E Clapham
(2018)
Cryo-EM structure of the polycystin 2-l1 ion channel
eLife 7:e36931.
https://doi.org/10.7554/eLife.36931

Share this article

https://doi.org/10.7554/eLife.36931

Categories and tags

Research organism

Further reading

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

    A conformational fingerprint for amyloidogenic light chains

    Cristina Paissoni, Sarita Puri ... Carlo Camilloni
    Research Article

    Both immunoglobulin light-chain (LC) amyloidosis (AL) and multiple myeloma (MM) share the overproduction of a clonal LC. However, while LCs in MM remain soluble in circulation, AL LCs misfold into toxic-soluble species and amyloid fibrils that accumulate in organs, leading to distinct clinical manifestations. The significant sequence variability of LCs has hindered the understanding of the mechanisms driving LC aggregation. Nevertheless, emerging biochemical properties, including dimer stability, conformational dynamics, and proteolysis susceptibility, distinguish AL LCs from those in MM under native conditions. This study aimed to identify a2 conformational fingerprint distinguishing AL from MM LCs. Using small-angle X-ray scattering (SAXS) under native conditions, we analyzed four AL and two MM LCs. We observed that AL LCs exhibited a slightly larger radius of gyration and greater deviations from X-ray crystallography-determined or predicted structures, reflecting enhanced conformational dynamics. SAXS data, integrated with molecular dynamics simulations, revealed a conformational ensemble where LCs adopt multiple states, with variable and constant domains either bent or straight. AL LCs displayed a distinct, low-populated, straight conformation (termed H state), which maximized solvent accessibility at the interface between constant and variable domains. Hydrogen-deuterium exchange mass spectrometry experimentally validated this H state. These findings reconcile diverse experimental observations and provide a precise structural target for future drug design efforts.

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

    Electrostatics of salt-dependent reentrant phase behaviors highlights diverse roles of ATP in biomolecular condensates

    Yi-Hsuan Lin, Tae Hun Kim ... Hue Sun Chan
    Research Article

    Liquid-liquid phase separation (LLPS) involving intrinsically disordered protein regions (IDRs) is a major physical mechanism for biological membraneless compartmentalization. The multifaceted electrostatic effects in these biomolecular condensates are exemplified here by experimental and theoretical investigations of the different salt- and ATP-dependent LLPSs of an IDR of messenger RNA-regulating protein Caprin1 and its phosphorylated variant pY-Caprin1, exhibiting, for example, reentrant behaviors in some instances but not others. Experimental data are rationalized by physical modeling using analytical theory, molecular dynamics, and polymer field-theoretic simulations, indicating that interchain ion bridges enhance LLPS of polyelectrolytes such as Caprin1 and the high valency of ATP-magnesium is a significant factor for its colocalization with the condensed phases, as similar trends are observed for other IDRs. The electrostatic nature of these features complements ATP’s involvement in π-related interactions and as an amphiphilic hydrotrope, underscoring a general role of biomolecular condensates in modulating ion concentrations and its functional ramifications.

    1. Structural Biology and Molecular Biophysics

    PROTAC-induced protein structural dynamics in targeted protein degradation

    Kingsley Y Wu, Ta I Hung, Chia-en A Chang
    Research Article

    PROteolysis TArgeting Chimeras (PROTACs) are small molecules that induce target protein degradation via the ubiquitin-proteasome system. PROTACs recruit the target protein and E3 ligase; a critical first step is forming a ternary complex. However, while the formation of a ternary complex is crucial, it may not always guarantee successful protein degradation. The dynamics of the PROTAC-induced degradation complex play a key role in ubiquitination and subsequent degradation. In this study, we computationally modelled protein complex structures and dynamics associated with a series of PROTACs featuring different linkers to investigate why these PROTACs, all of which formed ternary complexes with Cereblon (CRBN) E3 ligase and the target protein bromodomain-containing protein 4 (BRD4BD1), exhibited varying degrees of degradation potency. We constructed the degradation machinery complexes with Culling-Ring Ligase 4A (CRL4A) E3 ligase scaffolds. Through atomistic molecular dynamics simulations, we illustrated how PROTAC-dependent protein dynamics facilitating the arrangement of surface lysine residues of BRD4BD1 into the catalytic pocket of E2/ubiquitin cascade for ubiquitination. Despite featuring identical warheads in this PROTAC series, the linkers were found to affect the residue-interaction networks, and thus governing the essential motions of the entire degradation machine for ubiquitination. These findings offer a structural dynamic perspective on ligand-induced protein degradation, providing insights to guide future PROTAC design endeavors.