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. 2018 Aug 3;46(18):9793–9804. doi: 10.1093/nar/gky693

Figure 1.

Figure 1.

Aminoglycosides-decoding center structures at cryogenic (first and second rows) and ambient temperature (third row). (A) Sisomicin in the decoding center in a cryogenic sisomicin–30S decoding complex structure (PDB code: 6CAP). Unbiased Fo-Fc simple difference electron density map that belongs to sisomicin shown in blue mesh and contoured at 3σ level. (B) Superposition of the decoding center from a cryogenic sisomicin–30S decoding complex structure (salmon) and a cryogenic short RNA fragment-bound sisomicin structure (gray) (PDB code: 4F8U). Black arrows show minor local conformational changes in the 16S rRNA backbone. Asterisks mark positions of A1492 and A1493. (C) The h44–45 interaction in the cryogenic sisomicin-30S decoding complex is in an engaged: disengaged equilibrium. 2Fo-Fc electron density map of the h44-45 helices contoured at 1.5σ level and colored in blue. The unbiased Fo-Fc simple difference electron density map of the h45 region contoured at 3σ level and colored in green, which indicates the presence of a second alternate conformation. (D) The h44–45 interaction in the cryogenic paromomcyin–30S decoding complex is fully engaged (PDB code: 4DR4). (E) The h44–45 interaction in the cryogenic streptomycin–-30S decoding complex is fully disengaged (PDB code: 4DR6). (F) Superposed sisomicin, paromomycin and streptomycin–30S decoding complex structures. Sisomicin stabilizes a novel aminoglycoside-induced conformation by maintaining h45 in an equilibrium state (salmon). (G) Sisomicin in the decoding center of ambient temperature sisomicin–30S decoding complex structure (PDB code: 6CAR). Unbiased Fo-Fc electron density of the sisomicin calculated from ambient temperature SFX diffraction data shown in gray mesh and contoured at 3σ level. The structure will be colored in cyan throughout. (H) Superposition of the ambient (cyan) and cryogenic (salmon) sisomicin–30S decoding complex structures. (I) The h44–45 interaction in the ambient temperature sisomicin–30S decoding complex structure is in an engaged:disengaged equilibrium. 2Fo-Fc electron density map of the h44–45 helices contoured at 1.5σ level and colored in gray. The unbiased Fo-Fc electron density map of the h45 region contoured at 3σ level and colored in green indicates the presence of second alternate conformation.