The box H/ACA pseudouridine synthase complex guides modification of small nucleolar and Cajal body ribonucleoproteins (sno/scaRNAs), which are essential for maturation of the ribosome and spliceosome. The structure of a functional H/ACA complex containing L7Ae, Nop1 and Cbf5 proteins bound to the substrate and guide RNAs and with a catalytically rearranged substrate in the active site is now presented.