Abstract
The SEL1L-HRD1 complex represents the most conserved branch of endoplasmic reticulum (ER)-associated degradation (ERAD), a critical quality-control pathway that clears misfolded ER proteins. However, the molecular organization and pathogenic mechanisms of mammalian ERAD have remained elusive. Here, we report the cryo-EM structure of the core mammalian ERAD complex, comprising the ER lectin OS9, SEL1L, and the E3 ubiquitin ligase HRD1. The structure, validated by mutagenesis and crosslinking assays, reveals a dimeric assembly of the core complex in which SEL1L and OS9 form a claw-like configuration in the ER lumen that mediates substrate engagement, while HRD1 dimerizes within the membrane that may facilitate substrate translocation. Furthermore, pathogenic SEL1L mutations at the SEL1L-OS9 (Gly585Asp) and SEL1L-HRD1 (Ser658Pro) interfaces disrupt complex formation and impair ERAD activity. A newly identified disease-associated HRD1 variant (Ala91Asp), located in transmembrane helix 3, impairs HRD1 dimerization and substrate processing. These findings provide structural and functional insights for mammalian SEL1L-HRD1 ERAD and elucidate how mutations destabilizing this machinery contribute to human disease.
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The materials and reagents used are either commercially available or available upon the request. Proteomic data are available in a public database PRIDE (PXD043674 (http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD043674) and PXD041882). The cryo-EM map and the corresponding atomic model for the ERAD complex structure have been deposited under the accession codes EMD70448 (https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-70448) (consensus map), EMD-70452 (locally refined map) and 9OG0. All data related to this study are available in the main text or the supplementary material. Source data are provided with this paper.
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Acknowledgements
We thank the Qi, Jomaa, Sun labs (UVA), Arvan lab (UM), Drs. David Castle (UVA), Qinli Hu (UT Southwestern Medical Center), Maciej Gluc (UVA), Ruoya Ho (UVA), and Huan Bao (UVA) for technical support and insightful discussions; Drs. Michael Purdy and David Cooper (MEMC core, UVA), Haoran Yuan (UVA) and Riley Loyd (UVA) for assisting with the cryo-EM data collection and computational support; Dr. Chih-Chi Andrew Hu (Houston Methodist Hospital) for the Derlin-1 and Derlin-2 antibodies; and Drs. Fowzan Alkuraya and Khadijah Bakur for providing the information on the HRD1 A91D variant from the Lifera Omics Database. Cryo-EM data collection was conducted at the Molecular Electron Microscopy Core Facility (MEMC, RRID:SCR_019031) at the University of Virginia (UVA) School of Medicine (NIH G20-RR31199). We thank the Proteomics Resource Facility at University of Michigan Medical School for assisting proteomic assays. This work was supported by The Owens Family Foundation, the Searle Scholars Program (SSP-2023-106), American Cancer Society grant (#134088-IRG-19-143-33-IRG), and NIH 1R35 GM160490 to A.J.; NIH R01DK120047, R01DK120330, R35GM130292 to L.Q. L.L.L. was supported in part by National Ataxia Foundation Post-doctoral Fellowships NAF 918037. E.M. is supported by the cellular and molecular biology training program at UVA through NIH T32GM139787-3. L.E.Z. is supported by the American Heart Association Pre-doctoral Fellowship 25PRE1375196.
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This study was conceived by L.L.L., A.J. and L.Q. L.L.L. purified the ERAD core complex and collected cryo-EM data. E.M. processed cryo-EM data and built the atomic model. L.L.L. designed and performed all the biochemical experiments. L.E.Z. conducted the site directed point mutagenesis and plasmid preps. L.L.L. and L.Q. wrote the manuscript. All authors contributed to data analysis and final version of the manuscript.
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Lin, L.L., Maldosevic, E., Zhou, L.E. et al. Structural basis and pathological implications of the dimeric OS9-SEL1L-HRD1 ERAD Core Complex. Nat Commun (2026). https://doi.org/10.1038/s41467-026-68777-7
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DOI: https://doi.org/10.1038/s41467-026-68777-7
