Figure 1.

Structure of the Neurospora crassa QDE-2 MID domain. (A) Ribbon representation of the MID domain showing the positions of two bound sulphate ions (I and II) as sticks (red: oxygen; yellow: sulphur). Residues corresponding to those proposed by Kiriakidou et al (2007) to sandwich the m⁷GpppN cap are shown as purple sticks. Secondary structure elements are labelled. (B) Ribbon representation of an Af MID domain in complex with the 5′-end of a guide RNA (sticks), generated from Protein Data Bank entry 2bgg (Parker et al, 2005). (C) Superposition of the Nc QDE-2 MID domain onto the Af MID domain, illustrating the conservation of the Rossmann-like fold. (D) Structure-based sequence alignment of the Nc QDE-2 MID domain with archaeal (Af, Pf) and eubacterial (Aa, Tt) homologues, as well as with eukaryotic MID domains involved in the miRNA pathway. Positions involved in coordinating the two sulphate ions are shown in green. Positions proposed by Kiriakidou et al (2007) to bind the m⁷GpppN cap are shown in purple. The position proposed by Djuranovic et al (2010) to effect allosteric regulation of miRNA binding is shown in pink. Invariant or highly conserved positions are marked by an asterisk. Aa, Aquifex aeolicus; Af, Archaeoglobus fulgidus; MID, middle; miRNA, micro RNA; Nc, Neurospora crassa; Pf, Pyrococcus furiosus; QDE-2, quelling deficient 2; Tt, Thermus thermophilus.