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Published August 2022 | Supplemental Material
Journal Article Open

Structurally derived universal mechanism for the catalytic cycle of the tail-anchored targeting factor Get3

Abstract

Tail-anchored (TA) membrane proteins, accounting for roughly 2% of proteomes, are primarily targeted posttranslationally to the endoplasmic reticulum membrane by the guided entry of TA proteins (GET) pathway. For this complicated process, it remains unknown how the central targeting factor Get3 uses nucleotide to facilitate large conformational changes to recognize then bind clients while also preventing exposure of hydrophobic surfaces. Here, we identify the GET pathway in Giardia intestinalis and present the structure of the Get3–client complex in the critical postnucleotide-hydrolysis state, demonstrating that Get3 reorganizes the client-binding domain (CBD) to accommodate and shield the client transmembrane helix. Four additional structures of GiGet3, spanning the nucleotide-free (apo) open to closed transition and the ATP-bound state, reveal the details of nucleotide stabilization and occluded CBD. This work resolves key conundrums and allows for a complete model of the dramatic conformational landscape of Get3.

Additional Information

© 2022 Nature Publishing Group. Received 02 December 2021; Accepted 26 May 2022; Published 18 July 2022. We thank A. Malyutin, S. Chen, H. Scott, G. Lander and J. Kaiser for technical assistance. We thank S.-O.u Shan, R. Voorhees, D. Rees and A. Barlow for discussion and comments. We thank Luboš, Voleman and V. Dohnálek for their help with microscopy and phylogenetic analysis, respectively, V. Mechem for help with protein purification and crystallization, A. Barlow for help with the ATPase assay and Y. Liu for help with the in vitro TA protein capture assay. Crystallography data were collected at the SSRL beamline 12-2. We are grateful to the Gordon and Betty Moore Foundation for support of the Molecular Observatory at the California Institute of Technology. SSRL operations are supported by the US Department of Energy and US National Institutes of Health (NIH). (Cryo)Electron microscopy on the GiGet3–TA protein complex was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. A portion of this research was supported by NIH grant no. U24GM129547 and performed at the Pacific Northwest Center for Cryo-EM at Oregon Health & Science University and accessed through EMSL (grid.436923.9), a Department of Energy Office of Science User Facility sponsored by the Office of Biological and Environmental Research. Some computing resources were provided by the Extreme Science and Engineering Discovery Environment (XSEDE) resources, which is supported by the National Science Foundation grant no. Acl-1052574(108). Work in the United States was supported by the NIH grant nos. R01GM097572, R01GM125063 and DP1GM105385 to W.M.C. Work in the Czech Republic was supported by the Czech Science Foundation grant no. 20-25417S, a grant from Charles University Grant Agency (project no. 1396217) and the project 'Centre for research of pathogenicity and virulence of parasites' (grant no. CZ.02.1.01/0.0/0.0/16 019/0000759) funded by the European Regional Development Fund. S.M.S. was supported by National Science Foundation Graduate Research fellowship under grant no. 11444469. S.M.S. and M.Y.F. were supported by a NIH/National Research Service Award Training grant no. T32GM07616. Data availability: Atomic coordinates and structure factors for the apo GiGet3 crystal structure and ATP-bound GiGet3 have been deposited in the PDB under accession codes 7SPZ and 7SPY, respectively. The atomic coordinates and cryo-EM maps for the ADP-bound GiGet3–TA complex have been deposited to the PDB under the accession code 7SQ0 and Electron Microscopy Data Bank (EMDB) under the accession codes EMD-25374 (overall Get3–TA complex) and EMD-25373 (NBD of the Get3–TA complex). The apo GiGet3 cryo-EM map was deposited to the EMDB under the accession code EMD-25375. Source data are provided with this paper. Contributions: W.M.C., P.D. and M.Y.F. conceived the study. V.N. identified the Get3 homolog in Giardia and performed the verification using biochemical and cell biology methods. V.N. and S.M.S. identified other GET pathway components in Giardia and performed the phyologenetic analyses throughout eukaryotes. M.Y.F. performed the biochemistry to demonstrate GiSgt2 capture of TA proteins and identification of substrates in G. intestinalis. M.Y.F. prepared samples for structural studies, crystallized apo and ATP-bound GiGet3, and performed the all cryo-EM analyses and processing. M.Y.F., A.O.M. and W.M.C. refined the crystallography data and built the atomic model into the electron density. M.Y.F., A.O.M. and W.M.C. built the model into the GiGet3–TA complex cryo-EM map and M.Y.F. and W.M.C conducted the model building for the apo GiGet3 cryo-EM map. M.Y.F. and W.M.C. wrote the manuscript with input from all authors. All authors edited and approved the manuscript. The authors declare no competing interests. Peer review information: Nature Structural & Molecular Biology thanks the anonymous reviewers for their contribution to the peer review of this work. Peer reviewer reports are available. Primary Handling Editor: Florian Ullrich, in collaboration with the Nature Structural & Molecular Biology team.

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Additional details

Created:
August 22, 2023
Modified:
October 23, 2023