8K3O

Cryo-EM structure of 30S ribosome with cleaved AP-mRNA bound complex I

Summary for 8K3O

• Entry DOI: 10.2210/pdb8k3o/pdb
• EMDB information: 36854 36860 36868
• Descriptor: 30S ribosomal protein S2, 30S ribosomal protein S11, 30S ribosomal protein S12, ... (22 entities in total)
• Functional Keywords: ribosome, ap-mrna
• Biological source: Escherichia coli K-12; More
• Total number of polymer chains: 22
• Total formula weight: 801067.27

Authors

Afsar, M.,Shukla, A.,Ramachandran, R. (deposition date: 2023-07-16, release date: 2024-07-24, Last modification date: 2025-01-08)

Primary citation

Afsar, M.,Shukla, A.,Ali, F.,Maurya, R.K.,Bharti, S.,Kumar, N.,Sadik, M.,Chandra, S.,Rahil, H.,Kumar, S.,Ansari, I.,Jahan, F.,Habib, S.,Hussain, T.,Krishnan, M.Y.,Ramachandran, R.
Bacterial Rps3 counters oxidative and UV stress by recognizing and processing AP-sites on mRNA via a novel mechanism.
Nucleic Acids Res., 52:13996-14012, 2024

PubMed Abstract: Lesions and stable secondary structures in mRNA severely impact the translation efficiency, causing ribosome stalling and collisions. Prokaryotic ribosomal proteins Rps3, Rps4 and Rps5, located in the mRNA entry tunnel, form the mRNA helicase center and unwind stable mRNA secondary structures during translation. However, the mechanism underlying the detection of lesions on translating mRNA is unclear. We used Cryo-EM, biochemical assays, and knockdown experiments to investigate the apurinic/apyrimidinic (AP) endoribonuclease activity of bacterial ribosomes on AP-site containing mRNA. Our biochemical assays show that Rps3, specifically the 130RR131 motif, is important for recognizing and performing the AP-endoribonuclease activity. Furthermore, structural analysis revealed cleaved mRNA product in the 30S ribosome entry tunnel. Additionally, knockdown studies in Mycobacterium tuberculosis confirmed the protective role of Rps3 against oxidative and UV stress. Overall, our results show that prokaryotic Rps3 recognizes and processes AP-sites on mRNA via a novel mechanism that is distinct from eukaryotes.

PubMed: 39588766
DOI: 10.1093/nar/gkae1130

Experimental method

ELECTRON MICROSCOPY (3.88 Å)