8V85

60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Low-pass filtered locally refined map)

Summary for 8V85

• Entry DOI: 10.2210/pdb8v85/pdb
• Related: 8V83 8V84
• EMDB information: 43023
• Descriptor: ATP-dependent RNA helicase DBP10 (1 entity in total)
• Functional Keywords: rna binding, rna binding protein
• Biological source: Saccharomyces cerevisiae BY4741
• Total number of polymer chains: 1
• Total formula weight: 113126.47

Authors

Cruz, V.E.,Weirich, C.S.,Peddada, N.,Erzberger, J.P. (deposition date: 2023-12-04, release date: 2024-05-01)

Primary citation

Cruz, V.E.,Weirich, C.S.,Peddada, N.,Erzberger, J.P.
The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis.
Nat Commun, 15:3296-3296, 2024

PubMed Abstract: DEAD-box ATPases play crucial roles in guiding rRNA restructuring events during the biogenesis of large (60S) ribosomal subunits, but their precise molecular functions are currently unknown. In this study, we present cryo-EM reconstructions of nucleolar pre-60S intermediates that reveal an unexpected, alternate secondary structure within the nascent peptidyl-transferase-center (PTC). Our analysis of three sequential nucleolar pre-60S intermediates reveals that the DEAD-box ATPase Dbp10/DDX54 remodels this alternate base pairing and enables the formation of the rRNA junction that anchors the mature form of the universally conserved PTC A-loop. Post-catalysis, Dbp10 captures rRNA helix H61, initiating the concerted exchange of biogenesis factors during late nucleolar 60S maturation. Our findings show that Dbp10 activity is essential for the formation of the ribosome active site and reveal how this function is integrated with subsequent assembly steps to drive the biogenesis of the large ribosomal subunit.

PubMed: 38632236
DOI: 10.1038/s41467-024-47616-7

Experimental method

ELECTRON MICROSCOPY (2.9 Å)