Integrative modeling reveals the molecular architecture of the intraflagellar transport A (IFT-A) complex
- The University of Texas at Austin, United States
- Max Planck Institute of Molecular Cell Biology and Genetics, Germany
- 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.
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Author details
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.
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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Integrative modeling reveals the molecular architecture of the intraflagellar transport A (IFT-A) complex
eLife 11:e81977.
https://doi.org/10.7554/eLife.81977
