Extended Data Fig. 4: TXNL1 interacts with Rpn11 in a conformation-specific manner using its conserved C-terminal tail.

a) Sequence alignment of TXNL1 from uniport sequences using ENDscript at default settings: Homo sapiens (Q43396), Mus musculus (Q8CDN6), Gallus gallus (A0A1D5NUH1), Xenopus tropicalis (F6RTD9), Danio rerio (F6NTA0), Drosophila melanogaster (Q9VRP3), Caenorhabditis elegans (G5EES9) and Schizosaccharomyces pombe (Q9USR1). Red underlay shows conserved residues and blue boxes indicate similarity in amino acid identity. Residues in the C-terminal tail that mediate the interaction with Rpn11, including the terminal His, are highly conserved, except for fission yeast. b) Atomic models of Rpn11 with the Insert-1 (Ins-1) region in three conformations. The open loop conformation is found in resting-state proteasomes, the deubiquitination conformation with a β-hairpin is adopted upon ubiquitin binding to Rpn11, and the inhibitory, closed conformation is observed substrate-processing proteasomes. The three models are derived from our structure for the resting state RS.1 with TXNL1 in the forward orientation, the crystal structure of ubiquitin-bound Rpn11-Rpn8 (PDB ID: 5U4P), and our structure of the substrate-processing state PS_Rpt5, respectively. c) Space filling atomic model of PS_Rpt5 with the ribbon-represented PITH domain of TXNL1 in orange. The AlphaFold model for full-length TXNL1 is aligned by its PITH domain (light green) with the PITH domain in our structure and shows the TRX domain (dark green) with its catalytic CXXC motif (yellow spheres) close to the entrance of the ATPase motor. d) Overlay of the atomic models for PS_Rpt5 (Rpts in cyan) and PS_Rpt2 (Rpts in dark blue), aligned by Rpn11 (petrol), shows a movement of the Rpt4/Rpt5 coiled coil that significantly increases the gap to the Ins-1 loop (pink for PS_Rpt5, red for PS_Rpt2).