Figure 2
From: Domain swapping and SMYD1 interactions with the PWWP domain of human hepatoma-derived growth factor
Overall structure of the HDGF PWWP-SMYD1 complex. (A) Analyses of interactions of PWWP-SMYD1 complexes with various DNA lengths by size-exclusion chromatography (Superdex-200). The elution volume was further decreased with a longer length of SMYD1. From small to large elution volume: the PWWP-15 bp SMYD1 complex (blue line), PWWP-10 bp SMYD1 (red line), PWWP-5 bp SMYD1 (dashed line) and the apo PWWP domain (black line). (B) The domain-swapped structure of the PWWP-SMYD1 complex comprises a protein dimer (ribbon) and a 10-bp SMYD1 (orange stick) with interpretable density (blue mesh, 2F o-F c at 1 σ). The swapped domain “N/C terminus” consists of the N-terminus of chain A (green) and the C-terminus of chain B (marine), whereas the other swapped domain “C/N terminus” is composed of the C-terminus of chain A and the N-terminus of chain B. Loop1 (chain B) and loop4 (chain A) in the C/N terminus are involved in SMYD1 interactions. Two MPD molecules from the crystallization buffer are shown as black sticks (C) The unbiased initial density map (blue mesh, 2F o-F c at 1.3 σ) with the globular structure template from the apo PWWP domain shows the continuous structural feature traceable from Asp31 of chain B to the symmetry-related Asn43 of chain A. (D) The unambiguous electron density of the omit map (blue mesh, 2F o-F c at 1.3 σ) shows that the flexible loop2 in the globular monomeric apo PWWP domain is folded into the rigid αC helix (Gln35 – Ser40) to extend in a dimeric complex form. (E) The topology of secondary structures of the swapped PWWP-SMYD1 complex. Arrow: β-strand, cylinder: α-helix, solid line: loop. (F) Schematic representation of the dimeric swapped PWWP structure. The involved swapped region is shown in red and the other regions are in blue in one monomer (left). The other molecule of a dimer is shown in grey (right). The residues of the PWWP motif are indicated in stick, whereas the DNA-binding loops are shown in yellow. (G) Dimeric interactions in the dimeric PWWP-SMYD1 complex. The residues involved in interactions of domain swapping are shown as sticks with dashed lines between each other (chain A, green; chain B, marine). Numbers indicates the pair interactions are shown in Table S1.
