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CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P1
Structural highlights
FunctionELOB_HUMAN SIII, also known as elongin, is a general transcription elongation factor that increases the RNA polymerase II transcription elongation past template-encoded arresting sites. Subunit A is transcriptionally active and its transcription activity is strongly enhanced by binding to the dimeric complex of the SIII regulatory subunits B and C (elongin BC complex).[1] [2] The elongin BC complex seems to be involved as an adapter protein in the proteasomal degradation of target proteins via different E3 ubiquitin ligase complexes, including the von Hippel-Lindau ubiquitination complex CBC(VHL). By binding to BC-box motifs it seems to link target recruitment subunits, like VHL and members of the SOCS box family, to Cullin/RBX1 modules that activate E2 ubiquitination enzymes.[3] [4] Publication Abstract from PubMedTargeted protein degradation using proteolysis-targeting chimeras (PROTACs) offers a promising strategy to eliminate previously undruggable proteins. PROTACs are bifunctional molecules that link a target protein with an E3 ubiquitin ligase, enabling the formation of a ternary complex that promotes ubiquitination and subsequent proteasomal degradation. Although many ternary complex structures are available, understanding how structural features relate to PROTAC function remains challenging due to the dynamic nature of these complexes. Here we show that the interface between the target protein SMARCA2 and the E3 ligase VHL is conformationally flexible and stabilized by interactions involving disordered loops. Using molecular dynamics simulations and X-ray crystallography of SMARCA2-VHL complexes bound to five different PROTACs, we find that interfacial residues often adopt energetically suboptimal, or 'frustrated,' configurations. We further show that the degree of frustration correlates with experimentally measured cooperativity for a set of 11 PROTACs. These findings suggest that quantifying interface frustration provides a rational, structure-based approach to guiding PROTAC design. Frustration in the protein-protein interface plays a central role in the cooperativity of PROTAC ternary complexes.,Ma N, Bhattacharya S, Muk S, Jandova Z, Schmalhorst PS, Ghosh S, Le K, Diers E, Trainor N, Farnaby W, Roy MJ, Kofink C, Greb P, Weinstabl H, Ciulli A, Bader G, Sankar K, Bergner A, Vaidehi N Nat Commun. 2025 Sep 29;16(1):8595. doi: 10.1038/s41467-025-63713-7. PMID:41022846[5] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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