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. 2021 Mar 1;10:e65339. doi: 10.7554/eLife.65339

Figure 3. Structural overview of BLM-HDΔWHD in complex with compound 2.

(A) Schematic representation of the domain composition and respective amino acid boundaries for full-length human BLM and the two expression constructs used in this study BLM-HD and BLM-HDΔWHD. D1 and D2 = domains 1 and 2 of the helicase core; Zn = zinc-binding domain; WH = winged-helix; HRDC = Helicase and RNaseD C-terminal domain; RQC = RecQ C-terminal domain. (B and B inset) Molecular secondary structure cartoon highlighting components of a ‘pseudo-symmetrical’ dimer found in the asymmetric unit of BLM-HDΔWHD/Mg-ADP/2/ssDNA crystals, driven by partial complementarity of the single-stranded 15mer oligonucleotide at its 5’ end (DNA1 and DNA2, coloured orange and cyan respectively). Compound 2 (yellow-coloured spheres) binds to a small pocket found on the opposite side to that which binds nucleotide (grey-coloured spheres). (C, left) Molecular cartoon representation highlighting interactions made between 2 and BLM-HDΔWHD. Key amino acid residues are labelled and shown in stick representation, with carbon atoms coloured according to the schematic shown in panel A. Compound 2 is shown in stick representation, with carbon atoms coloured yellow. Potential hydrogen bonds are indicated by black dotted lines. (C, right) Modified LIGPLOT+ (Laskowski and Swindells, 2011) diagram of protein-compound interactions. See associated key for additional detail.

Figure 3.

Figure 3—figure supplement 1. Superposition of the structures of BLM-HD (PDB: 4CDG) and BLM-HDΔWHD using PyMOL (Schrödinger, 2020).

Figure 3—figure supplement 1.

Values for rmsd in Angstrom are shown, calculated over the indicated number of equivalent atoms. See associated key for details of colour scheme.
Figure 3—figure supplement 2. Isotherms for binding of BLM-HDΔWHD to (top) ssDNA-15mer and (bottom) compound 2 in the presence of ssDNA-15mer, as determined by MST.

Figure 3—figure supplement 2.

Values for Kd and 95% CI are given in each case. For all plots, data represent the mean of three technical replicates with error bars representing 1 SD.
Figure 3—figure supplement 3. Schematic summary of DNA-interactions made within the crystal lattice of the liganded complex (BLM-HDΔWHD + Mg-ADP + ssDNA-15mer + compound 2).

Figure 3—figure supplement 3.

Interaction network determined through by the PDBsum Generate webserver (PDBsum, 2021). Green solid lines represent hydrophobic / stacking interactions. Black dotted lines represent potential hydrogen bonds.