Integrative modeling reveals the molecular architecture of the intraflagellar transport A (IFT-A) complex

  1. Caitlyn L McCafferty  Is a corresponding author
  2. Ophelia Papoulas
  3. Mareike A Jordan
  4. Gabriel Hoogerbrugge
  5. Candice Nichols
  6. Gaia Pigino
  7. David W Taylor
  8. John B Wallingford
  9. Edward M Marcotte  Is a corresponding author
  1. The University of Texas at Austin, United States
  2. Max Planck Institute of Molecular Cell Biology and Genetics, Germany
  3. Human Technopole, Italy

Abstract

Intraflagellar transport (IFT) is a conserved process of cargo transport in cilia that is essential for development and homeostasis in organisms ranging from algae to vertebrates. In humans, variants in genes encoding subunits of the cargo-adapting IFT-A and IFT-B protein complexes are a common cause of genetic diseases known as ciliopathies. While recent progress has been made in determining the atomic structure of IFT-B, little is known of the structural biology of IFT-A. Here, we combined chemical cross-linking mass spectrometry and cryo-electron tomography with AlphaFold2-based prediction of both protein structures and interaction interfaces to model the overall architecture of the monomeric six-subunit IFT-A complex, as well as its polymeric assembly within cilia. We define monomer-monomer contacts and membrane-associated regions available for association with transported cargo, and we also use this model to provide insights into the pleiotropic nature of human ciliopathy-associated genetic variants in genes encoding IFT-A subunits. Our work demonstrates the power of integration of experimental and computational strategies both for multi-protein structure determination and for understanding the etiology of human genetic disease.

Data availability

Mass spectrometry proteomics data was deposited in the MassIVE/ProteomeXchange database (113) under accession number PXD032818. Cryo-tomography data was deposited in the Electron Microscopy Data Bank (114) under accession number EMD-26791. IFT-A models were deposited in the PDB-Dev database (115) as well as on Zenodo at doi: 10.5281/zenodo.7222413, along with additional supporting materials, including integrative modeling data and code.

Article and author information

Author details

  1. Caitlyn L McCafferty

    Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
    For correspondence
    clmccafferty@utexas.edu
    Competing interests
    The authors declare that no competing interests exist.
  2. Ophelia Papoulas

    Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Mareike A Jordan

    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Competing interests
    The authors declare that no competing interests exist.
  4. Gabriel Hoogerbrugge

    Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Candice Nichols

    Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Gaia Pigino

    Human Technopole, Milan, Italy
    Competing interests
    The authors declare that no competing interests exist.
  7. David W Taylor

    Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. John B Wallingford

    Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Edward M Marcotte

    Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
    For correspondence
    marcotte@utexas.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8808-180X

Funding

National Science Foundation (2019238253)

  • Caitlyn L McCafferty

National Institute of General Medical Sciences (R35GM122480)

  • Edward M Marcotte

National Institute of General Medical Sciences (R35GM138348)

  • David W Taylor

National Institute of Child Health and Human Development (HD085901)

  • John B Wallingford
  • Edward M Marcotte

Army Research Office (W911NF-12-1-0390)

  • Edward M Marcotte

Welch Foundation (F-1515)

  • Edward M Marcotte

Welch Foundation (F-1938)

  • David W Taylor

Max Planck Society

  • Mareike A Jordan
  • Gaia Pigino

Cancer Prevention and Research Institute of Texas (RR160088)

  • David W Taylor

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

Reviewing Editor

  1. Suzanne R Pfeffer, Stanford University, United States

Version history

  1. Preprint posted: July 5, 2022 (view preprint)
  2. Received: July 20, 2022
  3. Accepted: November 7, 2022
  4. Accepted Manuscript published: November 8, 2022 (version 1)
  5. Version of Record published: November 18, 2022 (version 2)

Copyright

© 2022, McCafferty 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. Caitlyn L McCafferty
  2. Ophelia Papoulas
  3. Mareike A Jordan
  4. Gabriel Hoogerbrugge
  5. Candice Nichols
  6. Gaia Pigino
  7. David W Taylor
  8. John B Wallingford
  9. Edward M Marcotte
(2022)
Integrative modeling reveals the molecular architecture of the intraflagellar transport A (IFT-A) complex
eLife 11:e81977.
https://doi.org/10.7554/eLife.81977

Share this article

https://doi.org/10.7554/eLife.81977

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