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. 2022 Jul 18;12:12241. doi: 10.1038/s41598-022-16193-4

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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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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A structural model for the linear ubiquitination of NEMO by the HOIP E3 ligase. The last four C-terminal amino acid residues of the proximal ubiquitin are not visible in the electron density map of the heteropentameric structure. The distance between the main chain carboxyl group of ubiquitin Arg72 and the sidechain ε-amino group of NEMO Lys285 is ~ 12 Å, which is sufficient to accommodate the last four C-terminal residues of ubiquitin (a.a. 73-76) and form an isopeptide bond. The electron density indicates the 2Fo–Fc map within 1.6 Å of the selected atoms (residues L71 and R72 of ubiquitin and L284-E286 of NEMO), contoured at 1.0 σ (B) Superimposition of the proximal ubiquitin on the acceptor ubiquitin bound to HOIP LDD (PDB ID: 4LJO), suggesting that ubiquitin can interact with NZF1 and RING2-LDD of HOIP. Ile44 residue of ubiquitin molecules are indicated as spheres (C) Superimposition of the three complex structures, including RING2-LDD/acceptor ubiquitin (PDB ID: 4LJO), RBR/donor ubiquitin (PDB ID: 5EDV), and NEMO/NZF1/ubiquitin (current structure) demonstrates a model for the site-specific ligation of linear ubiquitin chains to the NEMO substrate by HOIP. The gray spheres in the figures represent zinc ions.