The minor spliceosome mediates splicing of the rare but essential U12-type precursor messenger RNA. Here, we report the atomic features of the activated human minor spliceosome determined by cryo–electron microscopy at 2.9-angstrom resolution. The 5′ splice site and branch point sequence of the U12-type intron are recognized by the U6atac and U12 small nuclear RNAs (snRNAs), respectively. Five newly identified proteins stabilize the conformation of the catalytic center: The zinc finger protein SCNM1 functionally mimics the SF3a complex of the major spliceosome, the RBM48-ARMC7 complex binds the γ-monomethyl phosphate cap at the 5′ end of U6atac snRNA, the U-box protein PPIL2 coordinates loop I of U5 snRNA and stabilizes U5 small nuclear ribonucleoprotein (snRNP), and CRIPT stabilizes U12 snRNP. Our study provides a framework for the mechanistic understanding of the function of the human minor spliceosome.

较小的剪接体介导了罕见但必不可少的U12型前体信使RNA的剪接。在这里，我们报告了由冷冻电子显微镜在2.9埃分辨率下确定的激活的人类次要剪接体的原子特征。U12型内含子的5'剪接位点和分支点序列分别由U6atac和U12小核RNA（snRNA）识别。五个新发现的蛋白稳定了催化中心的构象：锌指蛋白SCNM1在功能上模仿了主要剪接体的SF3a复合物，RBM48-ARMC7复合物在U6atac snRNA（U6'的5'端结合了γ-单甲基磷酸酯帽）上。盒蛋白PPIL2协调U5 snRNA的环I，稳定U5小核糖核蛋白（snRNP），CRIPT稳定U12 snRNP。