Extended Data Figure 5: Structural details of eIF3d ‘RNA gate’ stabilizing interactions.
From: eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation
a–c, Structural overview of eIF3d with cut-away sections highlighting charged interactions stabilizing the closed ‘RNA gate’ conformation. No significant van der Waals interactions stabilize the closed gate conformation, supporting likely repositioning of the RNA gate before 5′ mRNA cap recognition. Charged interactions occur in three areas: a, at the beginning of the gate insertion sequence (gate beginning); b, at the tip of the unstructured loop (gate tip); and c, at an ‘arginine anchor’ point stabilizing the return of the loop insertion sequence to the α-helix shared with DXO family endonucleases. Residues are numbered according to the human eIF3d sequence, and all positions are conserved between human and N. vitripennis except S292N. eIF3d RNA gate residues are displayed with blue side chains and the residues making stabilizing contacts are coloured in green. 2Fo − Fc map regions are shown at 1.5σ.