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. 2023 Jan 2;30(5):584–593. doi: 10.1038/s41594-022-00905-5

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 5 — a, The 21 Å IFT-A average covering three repeats, unmasked to show that IFT-B (light blue) is averaged out with respect to IFT-A (alternating yellow) due to peridocity mismatch. b, The IFT-B1 average filtered to 12 Å and unmasked, to show that IFT-A (yellow) is averaged out with respect to IFT-B1 (alternating blue) due to periodicity mismatch. The red box indicates the location of the mask used for subclassification to generate the classes in d and e. c, Cartoon depicting the view in a, b, d and e. d, After classification of the IFT-A region in the IFT-B1 average, we find classes where IFT-A (alternating yellow) and IFT-B (alternating blue) are in sync. We see a new density (dark blue) linking IFT-B to IFT-A, which we designate as CC5 of IFT81/74. Bottom, cartoon representation of the density. e, A second class shows how the IFT81/74 connections (dark blue) adapt to the periodicity mismatch between IFT-A (alternating yellow) and IFT-B (alternating blue), by switching register with respect to IFT-A at the red arrow. Bottom, cartoon representation of the density. f, A top view of class A from classification of the IFT-A region in the IFT-B2 average. Inset, cartoon view. IFT-B1 (alternating light/dark blue) and IFT-B2 (alternating light/dark green) are joined by a new, unmodeled density corresponding to the C terminus of IFT172 (lime green). g, The same class as f, rotated 180° to view the same IFT172 density (lime green and transparent, with the AlphaFold2 model docked) interacting with IFT-A. The IFT-A complex is colored to highlight that the connecting density connects nonadjacent neighbors. Inset, cartoon view. h, The same view as in g, showing the AlphaFold2 IFT172 C terminus model (lime green) docked into the density along with our IFT-A model. IFT172 bridges the gap between IFT144 and IFT139. i, The same view as in h, with IFT172, IFT144 and IFT139 shown with surface charge depiction. The negatively charged IFT172 C terminus can make favorable ionic interactions with the positively charged IFT144 C terminus. j, Cartoon representation of the overall anterograde train structure, showing the two points of connection (dotted outlines). k, Cartoon representation depicting the proposed role of the flexible tethers in recruiting IFT-A complexes to nascent IFT trains.