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Updated: Sep 17, 2025

Functional Characterization of RING-Type E3 Ubiquitin Ligases In Vitro and In Planta
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Structural insights into the human HRD1 ubiquitin ligase complex

Liling Guo1,2, Guoyun Liu2, Jingjing He2

  • 1Department of General Medicine, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.

Nature Communications
|July 2, 2025
PubMed

Insights

The HRD1 ubiquitin ligase complex, crucial for endoplasmic reticulum-associated protein degradation (ERAD), undergoes significant structural changes upon interacting with Derlin proteins, revealing its molecular mechanism.

Area of Science:

  • Cell biology
  • Molecular biology
  • Structural biology

Background:

  • The endoplasmic reticulum (ER) clears defective proteins through the ER-associated protein degradation (ERAD) pathway.
  • The HRD1 ubiquitin ligase complex (HRD1, SEL1L, XTP3B, OS9, Derlins) is vital for ERAD substrate processing, but its molecular mechanisms remain unclear.

Purpose of the Study:

  • To determine the cryo-electron microscopy (cryo-EM) structure of the human HRD1-SEL1L-XTP3B complex.
  • To elucidate the structural basis of HRD1 complex function in ERAD.

Main Methods:

  • Cryo-electron microscopy (cryo-EM) at 3.3 Å resolution.
  • Analysis of the HRD1-SEL1L-XTP3B complex structure.
  • Investigation of complex conformational changes upon coexpression with Derlin proteins.
  • Cell-based functional assays.

Main Results:

  • The cryo-EM structure of the human HRD1-SEL1L-XTP3B complex (2:1:1 stoichiometry) was determined.
  • A trimmed N-glycan was observed interacting with XTP3B and SEL1L.
  • Complex formation with Derlin proteins induced dramatic conformational changes, breaking the HRD1 dimer and forming a new assembly with a four-helix bundle from SEL1L.
  • These changes suggest Derlin engagement induces local ER membrane curvature.

Conclusions:

  • The study provides the first high-resolution structure of the human HRD1-SEL1L-XTP3B complex.
  • Structural insights reveal how Derlin proteins modulate the HRD1 complex assembly and function.
  • This work lays the foundation for understanding the molecular mechanisms of mammalian ERAD.

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