Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Design and Semisynthesis of Ubiquitin Extension Probes for Structural Analysis of Cullin1-Mediated Substrate Polyubiquitination.
Journal, issue, pages	J Am Chem Soc, Vol. 147, Issue 27, Page 23878-23890, Year 2025
Publish date	Jul 9, 2025
Authors	Chuntong Li / Fangyu Zhao / Chong Zuo / Liying Zhang / Yangwode Jing / Xu Li / Guo-Chao Chu / Luyu Shi / Yingyue Zhang / Han Wang / Shuzhe Sun / Maoshen Sun / Huasong Ai / Lu-Jun Liang / Jinghong Li /
PubMed Abstract	Chemical trapping strategies have recently emerged as powerful approaches for investigating the structural dynamics of E3 ligase-catalyzed substrate ubiquitination. However, current ubiquitination- ...Chemical trapping strategies have recently emerged as powerful approaches for investigating the structural dynamics of E3 ligase-catalyzed substrate ubiquitination. However, current ubiquitination-derived probes are limited to studying substrate mono- or diubiquitination events. Probes capable of investigating how E3 ligases accommodate E2-Ub conjugates and ubiquitinated substrates to generate longer ubiquitin chains remain unexplored. In this work, we report the development of two Cullin1 E3 ligase (CRL1)-dependent probes, Extension Probe and Extension Probe, which mimic transient intermediates formed during CRL1-catalyzed K48-linked diubiquitin and tetraubiquitin chain formation on substrate p27. Notably, a chemoenzymatic semisynthetic strategy was devised to generate Extension Probe, involving the enzymatic conjugation of a preformed K48-linked diubiquitin to a synthetic Ub-p27-degron construct using the E2 conjugating enzyme UBE2K. Both Extension Probe and Extension Probe formed stable complexes with N8-CRL1 (comprising neddylated Cullin1-Rbx1 and the substrate receptor complex Skp1-Skp2-Cks1), facilitating structural analysis by chemical cross-linking mass spectrometry (CX-MS) and cryo-electron microscopy (cryo-EM). Our results indicate the presence of multiple distinct conformations of the catalytic module (comprising the RING domain of Rbx1, CDC34-Ub, and the acceptor ubiquitin) within the di- and tetraubiquitination complexes, while the conformation of the Cullin1-Skp1-Skp2-Cks1 subunit remains unchanged. In conclusion, this work expands the toolkit available for chemical trapping strategies and provides advanced insights into CRL-catalyzed substrate polyubiquitination.
External links	J Am Chem Soc / PubMed:40561458
Methods	EM (single particle)
Resolution	4.51 - 8.33 Å
Structure data	EMDB-60257: conformation 1 cryo-EM map of N8_Cullin1/Rbx1/Skp1/Skp2/Cks2/p27 in complex with Extension Probe-Ub2 at a resolution of 8.07 angstrom Method: EM (single particle) / Resolution: 8.07 Å EMDB-60258: conformation 2 cryo-EM map of N8_Cullin1/Rbx1/Skp1/Skp2/Cks2/p27 in complex with Extension Probe-Ub2 at a resolution of 7.64 angstrom Method: EM (single particle) / Resolution: 7.64 Å EMDB-60259: conformation 3 cryo-EM map of N8_Cullin1/Rbx1/Skp1/Skp2/Cks2/p27 in complex with Extension Probe-Ub2 at a resolution of 8.33 angstrom Method: EM (single particle) / Resolution: 8.33 Å EMDB-60260: cryo-EM map of N8_Cullin1/Rbx1/Skp1/Skp2/Cks2/p27 in complex with Extension Probe-Ub4 at a resolution of 7.05 angstrom Method: EM (single particle) / Resolution: 7.05 Å EMDB-60261: Skeleton cryo-EM map of N8_Cullin1/Rbx1/Skp1/Skp2/Cks2/p27 in complex with Extension Probe-Ub4 at a resolution of 4.51 angstrom Method: EM (single particle) / Resolution: 4.51 Å
Source	Homo sapiens (human)