Figure 4: Crystal structure of the paromomycin-bound partially rotated ribosome.
(a) Paromomycin binding within the (left) h44-decoding site and (right) within H69. 16S rRNA (blue), 23S rRNA H69 (grey) and paromomycin (h44—green; H69—teal) are shown, along with a (2Fobs−Fcalc) electron density map, calculated in PHENIX and contoured at 1.4 s.d. from the mean. Paromomycin and H69 rRNA contacts <3.5 Å are shown as dashed lines. (Inset) Paromomycin contacts within H69 are indistinguishable from those formed by neomycin (r.m.s.d.=0.412 Å). (b) Paromomycin induces global rearrangements of the 70S ribosome that are indistinguishable from those stabilized by neomycin. (Inset) View of the 30S subunit from the perspective of the 50S subunit. (Left) Difference in the vector shifts between equivalent RNA phosphorus atoms and protein Cα atoms in the unrotated compared with the partially rotated paromomycin-bound ribosome; (middle) superposition of the partially rotated neomycin-bound and partially rotated paromomycin-bound ribosomes. (Right) The fully rotated compared with the partially rotated paromomycin-bound ribosome. The vectors are colour coded as indicated in the scale. Ribosomes were superimposed using the 50S subunit as the frame of reference. 30S head domain: H; 30S body: B; 30S platform: P; 30S spur: Sp.
