5T6R

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

This is a non-PDB format compatible entry.

Summary for 5T6R

• Entry DOI: 10.2210/pdb5t6r/pdb
• Related: 5T62
• EMDB information: 8362 8368
• Descriptor: 25S Ribosomal RNA, 60S ribosomal protein L8-A, 60S ribosomal protein L9-A, ... (48 entities in total)
• Functional Keywords: ribosome biogenesis, 60s, nmd3, lsg1, tif6, cryo-em, ribosome
• Biological source: Saccharomyces cerevisiae; More
• Total number of polymer chains: 45
• Total formula weight: 2050798.01

Authors

Malyutin, A.G.,Musalgaonkar, S.,Patchett, S.,Frank, J.,Johnson, A.W. (deposition date: 2016-09-01, release date: 2017-02-08, Last modification date: 2024-03-13)

Primary citation

Malyutin, A.G.,Musalgaonkar, S.,Patchett, S.,Frank, J.,Johnson, A.W.
Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis.
EMBO J., 36:854-868, 2017

PubMed Abstract: 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.

PubMed: 28179369
DOI: 10.15252/embj.201696012

Experimental method

ELECTRON MICROSCOPY (4.2 Å)