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Figure 3
Analysis of the Qi site in the three different cryo-EM maps with the density contoured at 3σ. (a) The Qi site in the apo bc1 cryo-EM map shows minimal density (purple mesh) which does not correspond to any side chains or the haem bL group, suggesting noise within the map or that the natural substrate ubiquinone is bound in a small number of bc1 molecules. (b) The Qi site in the cryo-EM map of bc1–GSK932121. The inhibitor density (green) suggests there are two modes of inhibitor binding, accompanied by rotation around the oxygen–carbon bond. The binding pose shown in green agrees with the crystal structure, with the trifluoromethyl group pointing towards Met194. There is additional density which suggests that the trifluoromethoxyphenyl group could be rotated and point towards Asp228, revealing an additional mode of binding (shown in blue). (c) The Qi site in the cryo-EM map of bc1–SCR0911, with the inhibitor shown in pink and located in strong density. The inhibitor is expected to make a hydrogen-bond contact with His201 and strongly fits the density.

Volume 5| Part 2| March 2018| Pages 200-210
ISSN: 2052-2525