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. 2022 Dec 30;9(1):142–156. doi: 10.1038/s41477-022-01308-6

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© The Author(s) 2022

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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Extended Data Fig. 1 — P9 is a two-helix (H1, H2) peptide that spans the inner mitochondrial membrane from the matrix to the lumenal side by its transmembrane segment (TMSEG). For phylogenetic analysis, Arabidopsis P9 (At1g67785) was used to search the non-redundant protein sequences (nr) database at the National Center for Biotechnology Information (NCBI, “https://www.ncbi.nlm.nih.gov/”) using standard settings. >100 homologous sequences were identified below an E-value of 1e-4. All sequences were from seed plants (spermatophyta). Sixteen sequences were selected for building a multiple sequence alignment using Clustal Omega (https://www.ebi.ac.uk/Tools/msa/clustalo/); five sequences for dicots and monocots, respectively, and all identified sequences of other spermatophyta clades. Amino acid positions conserved in 16/16 sequences are highlighted in dark blue, amino acid positions conserved in ≥14/16 sequences in mid-blue and amino acid positions conserved in ≥10/16 sequences in light blue. Phylogenetic clades are indicated to the left of the alignment. The topology model of P9 is indicated above the alignment. The model was built into the cryo-EM density of the Arabidopsis I + III₂ supercomplex from valine at position 2 to alanine at position 56. The positions of its two alpha-helices are shown below the alignment. The complex III₂ interacting segment is shown in red. Residues K41, V45, V48, R49, L52 of Arabidopsis P9 that interact directly with complex III₂ are indicated by asterisks (see Fig. 4c and d). Accession of sequences. Arabidopsis thaliana: At1g67785, Brassica napus: CAF2186799, Medicago truncatula: XP_013446710, Malus domestica: XP_028959763, Trifolium pratense: XP_045824609, Pisum sativum: XP_050898094, Oryza sativa: NP_001392381, Hordeum vulgare: XP_044978029, Spirodela intermedia: CAA2619857, Phoenix dactylifera: XP_008797106, Asparagus officinalis: XP_020253321, Amborella trichopoda: XP_020527559, Nymphaea colorata: XP_031475842, Aristolochia fimbriata: KAG9445531, Picea sitchensis: ABK24944, Pinus taeda: AFG45619.