6AGB

Cryo-EM structure of yeast Ribonuclease P

Summary for 6AGB

• Entry DOI: 10.2210/pdb6agb/pdb
• EMDB information: 9616
• Descriptor: Ribonuclease P RNA, Ribonuclease P protein subunit RPR2, ZINC ION, ... (11 entities in total)
• Functional Keywords: ribonuclease p, rna-protein complex, hydrolase-rna complex, hydrolase/rna
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); More
• Total number of polymer chains: 11
• Total formula weight: 425186.39

Authors

Lan, P.,Tan, M.,Wu, J.,Lei, M. (deposition date: 2018-08-10, release date: 2018-10-17, Last modification date: 2024-03-27)

Primary citation

Lan, P.,Tan, M.,Zhang, Y.,Niu, S.,Chen, J.,Shi, S.,Qiu, S.,Wang, X.,Peng, X.,Cai, G.,Cheng, H.,Wu, J.,Li, G.,Lei, M.
Structural insight into precursor tRNA processing by yeast ribonuclease P.
Science, 362:-, 2018

PubMed Abstract: Ribonuclease P (RNase P) is a universal ribozyme responsible for processing the 5'-leader of pre-transfer RNA (pre-tRNA). Here, we report the 3.5-angstrom cryo-electron microscopy structures of RNase P alone and in complex with pre-tRNA The protein components form a hook-shaped architecture that wraps around the RNA and stabilizes RNase P into a "measuring device" with two fixed anchors that recognize the L-shaped pre-tRNA. A universally conserved uridine nucleobase and phosphate backbone in the catalytic center together with the scissile phosphate and the O3' leaving group of pre-tRNA jointly coordinate two catalytic magnesium ions. Binding of pre-tRNA induces a conformational change in the catalytic center that is required for catalysis. Moreover, simulation analysis suggests a two-metal-ion S2 reaction pathway of pre-tRNA cleavage. These results not only reveal the architecture of yeast RNase P but also provide a molecular basis of how the 5'-leader of pre-tRNA is processed by eukaryotic RNase P.

PubMed: 30262633
DOI: 10.1126/science.aat6678

Experimental method

ELECTRON MICROSCOPY (3.48 Å)