Supplementary Figure 6: Sequence and structure alignments of USP domains of CYLD, USP2, USP7 and USP21.
From: Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity
Structure alignment is based on superposition of the USP2, USP7 or USP21 complex on the zCYLD complex in the Met1 catalytic state using the PDBeFold server with the zCYLD USP domain as the reference (Cα r.m.s.d. values are 2.64, 2.70 and 2.72 Å over 219 residues in total, respectively).
(a) Structure-based sequence alignment of USP domains of zCYLD, human USP2 (PDB:2HD5), human USP7 (PDB:1NBF) and human USP21 (PDB:2Y5B). The drawing scheme is the same as that in Supplementary Fig. 4. Blue bars above the alignment correspond to the CYLD-specific truncations and insertion. The secondary structures of zCYLD and hUSP7 are shown above the alignment.
(b) Structure alignment of Ub molecules bound to USP2, USP7 and USP21 (colored yellow, green and blue, respectively). The USP domain of USP7 (colored red) is also shown as a representative USP domain.
(c) Structure alignment of Ub(dist) molecules bound to zCYLDΔBbox and USP7 (colored cyan and green, respectively). Ubprox and zCYLDΔBbox (colored pink and grey, respectively) are also shown.
(d) Structure alignment of zCYLDΔBbox in the Met1 catalytic state and USP7. The coloring scheme is the same as that in Supplementary Fig. 6b,c. Truncations (Fingers subdomain, the β-sheet intervening between β4 and β5 and the loop connecting β6 and β7) and an insertion (β9-β10 sheet) are indicated by blue circles.
