Structural insights into the ubiquitylation strategy of the oligomeric CRL2FEM1B E3 ubiquitin ligase

Cullin-RING E3 ubiquitin ligase (CRL) family members play critical roles in numerous biological processes and diseases including cancer and Alzheimer’s disease. Oligomerization of CRLs has been reported to be crucial for the regulation of their activities. However, the structural basis for its regulation and mechanism of its oligomerization are not fully known. Here, we present cryo-EM structures of oligomeric CRL2 FEM1B in its unneddylated state, neddylated state in complex with BEX2 as well as neddylated state in complex with FNIP1/FLCN. These structures reveal that asymmetric dimerization of N8-CRL2 FEM1B is critical for the ubiquitylation of BEX2 while FNIP1/FLCN is ubiquitylated by monomeric CRL2 FEM1B . Our data present an example of the asymmetric homo-dimerization of CRL. Taken together, this study sheds light on the ubiquitylation strategy of oligomeric CRL2 FEM1B according to substrates with different scales. Synopsis The structural basis and biological importance of cullin-RING ubiquitin ligase (CRL) oligomerization remain largely unclear. Here, high-resolution cryo-EM and biochemical data reveal that oligomerization of CRL2 FEM1B serves as a structural foundation for accommodating substrates of varying sizes. Cryo-EM structures show oligomeric CRL2 FEM1B in its unneddylated state and as neddylated form in complex with different substrates. RBX1 and CUL2 participate in the assembly of CRL2 FEM1B oligomers. Asymmetric homo-dimerization allows CRL2 FEM1B to ubiquitinate substrates with small scales, such as BEX2. Large substrates such as FNIP1/FLCN complexes are ubiquitinated by monomeric CRL2 FEM1B . Asymmetric homo-dimerization allows ubiquitination of substrates with small scales, while large substrates are targeted by monomeric CRL2-FEM1B E3.