Extended Data Fig. 7: Structural comparisons.
From: The eRF1 degrader SRI-41315 acts as a molecular glue at the ribosomal decoding center
a, Validation of SRI-41315 density. The model of the SRI-41315 binding site as in Fig. 2b docked into cryo-EM maps of the rabbit ribosome bound to eRF1(AAQ) without SRI-41315 (EMD-3038; left), of the human ribosome bound to eRF1 trapped by PF846 (EMD-22085; middle), or generated from particles selected for occupancy of the recycling factor ABCE1 (right), contoured at the indicated levels. Note: the left and middle maps lack SRI-41315, while the right map retains strong density corresponding to SRI-41315 coexisting with ABCE1 binding. b, The overall conformation of accommodated eRF1 is unchanged with SRI-41315. The model of eRF1(AAQ) bound to SRI-41315 (purple) aligned to eRF1(AAQ) without SRI-41315 (pink; PDB 3JAG) or eRF1 trapped on ribosomes by PF846 (blue; 6XA1). The N, M, and C domains (left), the GGQ motif, and the SRI-41315 binding site (right) are indicated. c, Docking of related small molecule eRF1 degraders in the SRI-41315 binding site. d, SRI-41315 binding region of eRF1 (PDB 1DT9) colored by conservation. Note: Met51 is less conserved than Tyr125 and other residues required for stop codon decoding. e, SRI-41315 does not change ABCE1 conformation. Alignment of ABCE1 on termination complexes without (pink; PDB 3JAG) or with (dark blue) SRI-41315. Iron-sulfur clusters are colored by heteroatoms. f, ABCE1 is slightly stabilized on ribosomes with SRI-41315. Total, soluble, and ribosomal fractions of translation reactions without or with 100 µM SRI-41315 as in Fig. 1c were analyzed by SDS-PAGE and immunoblotting for ABCE1, representative of 3 replicates with similar results.
