7R7A

State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model

This is a non-PDB format compatible entry.

Summary for 7R7A

• Entry DOI: 10.2210/pdb7r7a/pdb
• Related: 7NAC 7NAD 7NAF 7R6K 7R6Q 7R72
• EMDB information: 24269 24270 24271 24280 24286 24290 24296
• Descriptor: 25S rRNA, rRNA-processing protein EBP2, 60S ribosomal protein L13-A, ... (58 entities in total)
• Functional Keywords: ribosome biogenesis, dead-box atpases, methyltransferase, nucleolus, ribosome
• Biological source: Saccharomyces cerevisiae BY4741; More
• Total number of polymer chains: 57
• Total formula weight: 2924753.07

Authors

Cruz, V.E.,Sekulski, K.,Peddada, N.,Erzberger, J.P. (deposition date: 2021-06-24, release date: 2022-11-09, Last modification date: 2024-06-05)

Primary citation

Cruz, V.E.,Sekulski, K.,Peddada, N.,Sailer, C.,Balasubramanian, S.,Weirich, C.S.,Stengel, F.,Erzberger, J.P.
Sequence-specific remodeling of a topologically complex RNP substrate by Spb4.
Nat.Struct.Mol.Biol., 29:1228-1238, 2022

PubMed Abstract: DEAD-box ATPases are ubiquitous enzymes essential in all aspects of RNA biology. However, the limited in vitro catalytic activities described for these enzymes are at odds with their complex cellular roles, most notably in driving large-scale RNA remodeling steps during the assembly of ribonucleoproteins (RNPs). We describe cryo-EM structures of 60S ribosomal biogenesis intermediates that reveal how context-specific RNA unwinding by the DEAD-box ATPase Spb4 results in extensive, sequence-specific remodeling of rRNA secondary structure. Multiple cis and trans interactions stabilize Spb4 in a post-catalytic, high-energy intermediate that drives the organization of the three-way junction at the base of rRNA domain IV. This mechanism explains how limited strand separation by DEAD-box ATPases is leveraged to provide non-equilibrium directionality and ensure efficient and accurate RNP assembly.

PubMed: 36482249
DOI: 10.1038/s41594-022-00874-9

Experimental method

ELECTRON MICROSCOPY (3.04 Å)