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	Cryo-EM structure of the human COP1-DET1 ubiquitin ligase complex.
Journal, issue, pages	Nat Commun, Vol. 17, Issue 1, Page 543, Year 2026
Publish date	Jan 15, 2026
Authors	Shan Wang / Fei Teng / Goran Stjepanovic / Feng Rao / Ming-Yuan Su /
PubMed Abstract	Ubiquitin modifications regulate fundamental cellular activities by modulating protein stability and function. The ubiquitin ligase COP1, which is present across species from plants to humans, plays ...Ubiquitin modifications regulate fundamental cellular activities by modulating protein stability and function. The ubiquitin ligase COP1, which is present across species from plants to humans, plays a crucial role in the ubiquitination of developmental transcription factors. While COP1 can function independently, it can also be incorporated into CULLIN4-RING ubiquitin ligase (CRL4) complexes through the DET1 adaptor protein. Despite its biological significance, the structural and functional mechanisms of COP1 and DET1-containing complexes remains poorly understood. Here we present the cryo-electron microscopy structures of human COP1 in complex with DDB1-DDA1-DET1 and Ube2e2, revealing an inactive stacked assembly state. Co-expression with COP1 substrates including c-Jun or ETS2 disrupts this configuration, inducing a conformational rearrangement into a distinct dimeric state that allows substrate access. Structural modelling identifies the spatial organization of COP1 WD40 domains where substrate recruits. DET1 serves as a structural scaffold, bridging COP1 and Ube2e2 to initiate potential ubiquitin addition on substrates, while DDB1 recruits the CULLIN4-RBX1 complex to facilitate Ube2d3-mediated ubiquitin chain elongation. These results reveal the dynamic interplay between the structural states of the CRL4 E3 ligase complex and its substrate specific activation mechanism, offering mechanistic insights into ubiquitination regulation and a basis for future studies on E3 ligase dynamics.
External links	Nat Commun / PubMed:41540009 / PubMed Central
Methods	EM (single particle)
Resolution	2.65 - 4.99 Å
Structure data	63371 9ltj EMDB-63371, PDB-9ltj: Cryo-EM structure of DDB1-DDA1-DET1 complex Method: EM (single particle) / Resolution: 2.65 Å 63372 9ltl EMDB-63372, PDB-9ltl: Cryo-EM structure of DDB1-DDA1-DET1 complex Method: EM (single particle) / Resolution: 2.93 Å 63374 9lto EMDB-63374, PDB-9lto: Cryo-EM structure of DDB1-DDA1-DET1-Ube2e2 complex Method: EM (single particle) / Resolution: 2.92 Å 63375 9ltr EMDB-63375, PDB-9ltr: Cryo-EM structure of dimeric DDB1-DDA1-DET1-Ube2e2-COP1 complex Method: EM (single particle) / Resolution: 3.03 Å 63383 9ltw EMDB-63383, PDB-9ltw: protein structure of DDB1-DDA1-DET1 Method: EM (single particle) / Resolution: 3.25 Å 63385 9ltz EMDB-63385, PDB-9ltz: protein structure of DDB1-DDA1-DET1-Ube2e2 complex Method: EM (single particle) / Resolution: 3.26 Å 63386 9lu1 EMDB-63386, PDB-9lu1: protein structure of DDB1-DDA1-DET1-Ube2e2 bound to COP1 dimer Method: EM (single particle) / Resolution: 3.62 Å 63397 9lul EMDB-63397, PDB-9lul: Local refinement of stacked like DDB1-DDA1-DET1-Ube2e2-COP1 complex (layer 1) Method: EM (single particle) / Resolution: 4.99 Å 63565 9m0y EMDB-63565, PDB-9m0y: Local refinement of stacked like DDB1-DDA1-DET1-Ube2e2-COP1 complex (layer 2) Method: EM (single particle) / Resolution: 4.25 Å 65758 9w90 EMDB-65758, PDB-9w90: DDB1-DDA1-DET1-Ube2e2-COP1-c-Jun-STK40 complex Method: EM (single particle) / Resolution: 3.7 Å
Source	homo sapiens (human)
Keywords	LIGASE / E3 ligase component / E3 ligase