DomainFit: Identification of protein domains in cryo-EM maps at intermediate resolution using AlphaFold2-predicted models

Jerry Gao; Maxwell Tong; Chinkyu Lee; Jacek Gaertig; Thibault Legal; Khanh Huy Bui

doi:10.1016/j.str.2024.04.017

DomainFit: Identification of protein domains in cryo-EM maps at intermediate resolution using AlphaFold2-predicted models

Structure. 2024 May 6:S0969-2126(24)00143-6. doi: 10.1016/j.str.2024.04.017. Online ahead of print.

Authors

Jerry Gao¹, Maxwell Tong¹, Chinkyu Lee², Jacek Gaertig², Thibault Legal³, Khanh Huy Bui⁴

Affiliations

¹ Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Montréal, QC H3A 0C7, Canada; Centre de recherche en biologie structurale, McGill University, Montréal, QC H3G 0B1, Canada.
² Department of Cellular Biology, University of Georgia, Athens 30602-2607, GA, USA.
³ Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Montréal, QC H3A 0C7, Canada; Centre de recherche en biologie structurale, McGill University, Montréal, QC H3G 0B1, Canada. Electronic address: thibault.legal@mcgill.ca.
⁴ Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Montréal, QC H3A 0C7, Canada; Centre de recherche en biologie structurale, McGill University, Montréal, QC H3G 0B1, Canada. Electronic address: huy.bui@mcgill.ca.

PMID: 38754431
DOI: 10.1016/j.str.2024.04.017

Abstract

Cryoelectron microscopy (cryo-EM) has revolutionized the structural determination of macromolecular complexes. With the paradigm shift to structure determination of highly complex endogenous macromolecular complexes ex vivo and in situ structural biology, there are an increasing number of structures of native complexes. These complexes often contain unidentified proteins, related to different cellular states or processes. Identifying proteins at resolutions lower than 4 Å remains challenging because side chains cannot be visualized reliably. Here, we present DomainFit, a program for semi-automated domain-level protein identification from cryo-EM maps, particularly at resolutions lower than 4 Å. By fitting domains from AlphaFold2-predicted models into cryo-EM maps, the program performs statistical analyses and attempts to identify the domains and protein candidates forming the density. Using DomainFit, we identified two microtubule inner proteins, one of which contains a CCDC81 domain and is exclusively localized in the proximal region of the doublet microtubule in Tetrahymena thermophila.

Keywords: AlphaFold2 modeling; cilia; cryo-EM; cryo-ET; domain identification; doublet; microtubule inner protein; protein identification; subtomogram averaging.