9KHT
cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked triUb (dimeric conformation)
Summary for 9KHT
| Entry DOI | 10.2210/pdb9kht/pdb |
| EMDB information | 62354 |
| Descriptor | Polyubiquitin-C, Ubiquitin, E4 ubiquitin-protein ligase UFD2, ... (4 entities in total) |
| Functional Keywords | e4 enzyme, ub ligase, ufd2, ubc4, branching, k48/29, ligase |
| Biological source | Homo sapiens (human) More |
| Total number of polymer chains | 12 |
| Total formula weight | 320169.23 |
| Authors | Ai, H.S.,Tong, Z.B.,Liu, L. (deposition date: 2024-11-11, release date: 2025-07-30, Last modification date: 2025-08-27) |
| Primary citation | Tong, Z.,Wu, X.,Cai, H.,Wu, S.,Zhang, T.,Deng, Z.,Xu, Z.,Yuan, R.,Ai, H.,Liu, L.,Pan, M. Structural basis for E4 enzyme Ufd2-catalyzed K48/K29 branched ubiquitin chains. Nat.Chem.Biol., 2025 Cited by PubMed Abstract: E4 enzymes amplify and remodel ubiquitin chain signals beyond the conventional E1-E2-E3 cascade. The first identified E4 enzyme Ufd2 preferentially catalyzes K48/K29 branched ubiquitin chains, yet the structural mechanism remains unknown. Here, we combined chemical biology and cryo-electron microscopy to visualize stable intermediates in Ufd2 loading ubiquitin at K48 of proximal ubiquitin on K29-linked di- and triubiquitin. Our data reveal that the core region of Ufd2 functions as an unprecedented K29 diubiquitin binding domain, interacting extensively with proximal and distal ubiquitin, which orients the K48 site of proximal ubiquitin toward the active site of Ubc4, facilitating K48/K29 branched ubiquitin chain formation. We also identified a unique dimeric conformation where dimerized Ufd2 and Ubc4 stabilize each other's distal ubiquitin during branching on K29 triubiquitin. Our findings provide mechanistic insights into the assembly of K48/K29 branched ubiquitin chains by the E4 enzyme Ufd2 and highlight the spatial cooperation among multiple pairs of ubiquitin-related enzymes on longer ubiquitin chains. PubMed: 40817136DOI: 10.1038/s41589-025-01985-2 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (4.85 Å) |
Structure validation
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