Structural intermediates in the low pH-induced transition of influenza hemagglutinin
Fig 4
Structure changes in the stem region of the pH 5.2 conformation C.
(A) Ribbon and surface rendered diagrams showing the fitted beta sheet, C-terminal helices of the stem region (residues 23–37 and 126–172 of HA2 subunits and 9–17 of HA1 subunits) in the pH 5.2 conformation C density map low-pass filtered to 7 Å. The fitted structures in the HA density are colored hot pink, cornflower blue and orange, respectively. The head and central helices are shown in gray. The low-pass filtered pH 5.2 conformation C density map is contoured at 6 σ and shown as a semi-transparent surface. Zoom-in views of the fitted region are shown at the right. The fitting was done in Chimera by treating the beta sheet and the C-terminal helices of the stem region as a rigid body and by maximizing the density values around the fitted atoms [52]. (B) Models are shown as the same as in (A) with a “zero-out” density map of the pH 5.2 conformation C shown as solid surfaces in cyan. The “zero-out” density map was calculated by setting the density value within 3 Å around the atoms of the model to zero. (C) Models of pH 5.2 conformation C (hot pink) and pH 5.2 conformation A (gray) are superimposed by using the head domains. The steric clashes between the central helices of the pH 5.2 conformation C and the stem region (fusion peptide and beta sheets) of the pH 5.2 conformation A are shown in blue. (D) Structure comparisons of the stem regions under different pH conditions. The stem region rotates and shifts upon the decrease of the pH. The shift of the C terminus is approximately 15 Å and the shift of the center of mass is approximately 7 Å. The rotation of the C terminus with the membrane-distal end of each central helix as the pivot point (residue Arg76) is approximately 9.5 degrees.