Fig. 3: Structural basis of K48-linked di-Ub recognition by RPN2.
From: Structural basis of K11/K48-branched ubiquitin chain recognition by the human 26S proteasome
a Structural alignment of RPN1 (orchid) and RPN2 (fuchsia) focusing on the helical Ub binding motifs (highlighted in blue and hot pink, respectively). The alternating K11-K48-linked di-Ub is colored following the same scheme as in Fig. 1e. The structure of RPN1 is taken from the PDB entry 6J2N. The structure of the RPN2 in complex with the K11-K48-linked di-Ub is taken from the ED:Ub4 state in this study. b Expanded view of the K48-linked di-Ub in complex with RPN2. The conserved E538 and D564 are highlighted by red ovals. The inter-chain hydrogen bonds and salt bridges are shown in dashed white lines and dashed green lines, respectively. c LOGO representation of the sequence conservation of the K48-linkage binding motif shared by RPN2 and RPN1. The conserved acidic residues are indicated in red, and the other conserved hydrophobic residues are highlighted in black below the sequence alignment. They are numbered according to the sequence of RPN2.
