Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis

During ribosome biogenesis in eukaryotes, nascent subunits are exported to the cytoplasm in a functionally inactive state. 60S subunits are activated through a series of cytoplasmic maturation events. The last known events in the cytoplasm are the release of Tif6 by Efl1 and Sdo1 and the release of the export adapter, Nmd3, by the GTPase Lsg1. Here, we have used cryo‐electron microscopy to determine the structure of the 60S subunit bound by Nmd3, Lsg1, and Tif6. We find that a central domain of Nmd3 mimics the translation elongation factor eIF5A, inserting into the E site of the ribosome and pulling the L1 stalk into a closed position. Additional domains occupy the P site and extend toward the sarcin–ricin loop to interact with Tif6. Nmd3 and Lsg1 together embrace helix 69 of the B2a intersubunit bridge, inducing base flipping that we suggest may activate the GTPase activity of Lsg1. Synopsis Cryo‐EM structures of the yeast 60S subunit bound to assembly factors Nmd3, Lsg1, and Tif6 reveal the conformational rearrangements that take place during final ribosome maturation in the cytoplasm. Structure of the 60S subunit export adapter Nmd3 and the GTPase Lsg1 at 3.1–4.5 Å resolution. Nmd3 spans the intersubunit interface of the 60S subunit from the L1 stalk through the E and P sites to Tif6. An eIF5A‐like domain of Nmd3 induces closure of the L1 stalk. Nmd3 must retract from the P site to allow binding of Sdo1 and final maturation steps to occur. Activation of Lsg1 GTPase requires both Nmd3 and 60S subunits. Lsg1 binding to helix 69 causes base flipping of G2661. Graphical Abstract Cryo‐EM structures of the yeast 60S subunit bound to assembly factors Nmd3, Lsg1, and Tif6 reveal the conformational rearrangements that take place during final ribosome maturation in the cytoplasm.