9KEN

cryo-EM structure of TRIP12 in complex with K29/48 branched-triUb

Summary for 9KEN

• Entry DOI: 10.2210/pdb9ken/pdb
• EMDB information: 62292
• Descriptor: Ubiquitin, Ubiquitin K29C, E3 ubiquitin-protein ligase TRIP12 (3 entities in total)
• Functional Keywords: hect e3 ligase, branching, k29/48, ligase
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 3
• Total formula weight: 197909.58

Authors

Ai, H.S.,Wu, X.W.,Liu, L. (deposition date: 2024-11-05, release date: 2025-08-06)

Primary citation

Wu, X.,Ai, H.,Mao, J.,Cai, H.,Liang, L.J.,Tong, Z.,Deng, Z.,Zheng, Q.,Liu, L.,Pan, M.
Structural visualization of HECT-type E3 ligase Ufd4 accepting and transferring ubiquitin to form K29/K48-branched polyubiquitination.
Nat Commun, 16:4313-4313, 2025

PubMed Abstract: The K29/K48-linked ubiquitination generated by the cooperative catalysis of E3 ligase Ufd4 and Ubr1 is an enhanced protein degradation signal, in which Ufd4 is responsible for introducing K29-linked ubiquitination to K48-linked ubiquitin chains to augment polyubiquitination. How HECT-E3 ligase Ufd4 mediates the ubiquitination event remains unclear. Here, we biochemically determine that Ufd4 preferentially catalyses K29-linked ubiquitination on K48-linked ubiquitin chains to generate K29/K48-branched ubiquitin chains and capture structural snapshots of Ub transfer cascades for Ufd4-mediated ubiquitination. The N-terminal ARM region and HECT domain C-lobe of Ufd4 are identified and characterized as key structural elements that together recruit K48-linked diUb and orient Lys29 of its proximal Ub to the active cysteine of Ufd4 for K29-linked branched ubiquitination. These structures not only provide mechanistic insights into the architecture of the Ufd4 complex but also provide structural visualization of branched ubiquitin chain formation by a HECT-type E3 ligase.

PubMed: 40341121
DOI: 10.1038/s41467-025-59569-6

Experimental method

ELECTRON MICROSCOPY (3.63 Å)