9B5W
Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 1 map and model from cluster 5 (ATP/Mg)
This is a non-PDB format compatible entry.
Summary for 9B5W
| Entry DOI | 10.2210/pdb9b5w/pdb |
| Related | 9B5C 9B5D 9B5F 9B5G 9B5H 9B5I 9B5J 9B5K 9B5L 9B5M 9B5N 9B5O 9B5P 9B5Q 9B5R 9B5S 9B5T 9B5U 9B5V 9B5X |
| EMDB information | 44227 |
| Descriptor | Ubiquitin-activating enzyme E1 1, Ubiquitin-conjugating enzyme E2 4, Ubiquitin, ... (6 entities in total) |
| Functional Keywords | ubiquitin, e1, e2, uba1, ubc4, transthioesterification, thioester, transthiolation, tetrahedral intermediate, adenylation, inhibitor, ligase, nucleus, phosphoprotein, ubl conjugation pathway, ubl, atp, atp-binding, amp, nucleotide-binding, isopeptide bond |
| Biological source | Schizosaccharomyces pombe 972h- More |
| Total number of polymer chains | 3 |
| Total formula weight | 138217.24 |
| Authors | Kochanczyk, T.,Lima, C.D. (deposition date: 2024-03-22, release date: 2024-06-05, Last modification date: 2024-09-25) |
| Primary citation | Kochanczyk, T.,Hann, Z.S.,Lux, M.C.,Delos Reyes, A.M.V.,Ji, C.,Tan, D.S.,Lima, C.D. Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633:216-223, 2024 Cited by PubMed Abstract: Transthiolation (also known as transthioesterification) reactions are used in the biosynthesis of acetyl coenzyme A, fatty acids and polyketides, and for post-translational modification by ubiquitin (Ub) and ubiquitin-like (Ubl) proteins. For the Ub pathway, E1 enzymes catalyse transthiolation from an E1~Ub thioester to an E2~Ub thioester. Transthiolation is also required for transfer of Ub from an E2~Ub thioester to HECT (homologous to E6AP C terminus) and RBR (ring-between-ring) E3 ligases to form E3~Ub thioesters. How isoenergetic transfer of thioester bonds is driven forward by enzymes in the Ub pathway remains unclear. Here we isolate mimics of transient transthiolation intermediates for E1-Ub(T)-E2 and E2-Ub(T)-E3 complexes (where T denotes Ub in a thioester or Ub undergoing transthiolation) using a chemical strategy with native enzymes and near-native Ub to capture and visualize a continuum of structures determined by single-particle cryo-electron microscopy. These structures and accompanying biochemical experiments illuminate conformational changes in Ub, E1, E2 and E3 that are coordinated with the chemical reactions to facilitate directional transfer of Ub from each enzyme to the next. PubMed: 39143218DOI: 10.1038/s41586-024-07828-9 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.96 Å) |
Structure validation
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