Pseudouridine, the most abundant form of RNA modification, is known to play important roles in ribosome function. Mutations in human DKC1, the pseudouridine synthase responsible for catalyzing the ribosome RNA modification, cause translation deficiencies and are associated with a complex cancer predisposition. The structural basis for how pseudouridine impacts ribosome function remains uncharacterized. Here, we characterized structures and conformations of a fully modified and a pseudouridine-free ribosome from Saccharomyces cerevisiae in the absence of ligands or when bound with translocation inhibitor cycloheximide by electron cryomicroscopy. In the modified ribosome, the rearranged N1 atom of pseudouridine is observed to stabilize key functional motifs by establishing predominately water-mediated close contacts with the phosphate backbone. The pseudouridine-free ribosome, however, is devoid of such interactions and displays conformations reflective of abnormal inter-subunit movements. The erroneous motions of the pseudouridine-free ribosome may explain its observed deficiencies in translation.

假尿苷是最丰富的 RNA 修饰形式，已知在核糖体功能中发挥重要作用。人类 DKC1（负责催化核糖体 RNA 修饰的假尿苷合酶）的突变会导致翻译缺陷，并与复杂的癌症易感性相关。假尿苷如何影响核糖体功能的结构基础仍然未知。在这里，我们表征了来自酿酒酵母的完全修饰且不含假尿苷的核糖体的结构和构象在没有配体的情况下或当通过电子冷冻显微镜与易位抑制剂放线菌酮结合时。在修饰的核糖体中，观察到重排的假尿苷 N1 原子通过与磷酸主链建立主要由水介导的紧密接触来稳定关键功能基序。然而，不含假尿苷的核糖体缺乏这种相互作用，并且显示出反映异常亚基间运动的构象。无假尿苷核糖体的错误运动可以解释其观察到的翻译缺陷。