9H3G

Structure of the Arabidopsis thaliana 80S ribosome in complex with P- and E-site tRNAs and mRNA

This is a non-PDB format compatible entry.

Summary for 9H3G

• Entry DOI: 10.2210/pdb9h3g/pdb
• EMDB information: 51820
• Descriptor: Ribosomal RNA 5.8S, Small ribosomal subunit protein eS26y, Large ribosomal subunit protein uL6z/uL6y, ... (86 entities in total)
• Functional Keywords: plant, thermospermine, methylation, rrna modification, ribosome
• Biological source: Arabidopsis thaliana (thale cress); More
• Total number of polymer chains: 80
• Total formula weight: 3195456.90

Authors

Faille, A.,Warren, A.J. (deposition date: 2024-10-16, release date: 2026-02-04, Last modification date: 2026-02-25)

Primary citation

Ko, D.,Ruonala, R.,Faille, A.,Hellmann, E.,Help, H.,Liu, H.,Nielsen, R.,Haakonsson, A.,De Diego, N.,Paatero, A.,Shcherbii, M.V.,Stefanowicz, K.,Cavar Zeljkovic, S.,Drud Lundager Rasmussen, T.,Novak, O.,Bodi, Z.,Eswaran, G.,Wybouw, B.,Bourdon, M.,Urbez, C.,Liu, X.,Salokas, K.,Ohman, T.,Waldie, T.,Toronen, P.,El-Showk, S.,Balcerowicz, M.,Besnard, F.,Liu, X.,Perkins, P.,Mazzoni-Putman, S.,Vainonen, J.P.,Sierla, M.,Frilander, M.J.,Mandrup, S.,Vernoux, T.,Ljung, K.,Ferrando, A.,Blazquez, M.A.,Holm, L.,Fray, R.,Varjosalo, M.,Leyser, O.,Paavilainen, V.O.,Mahonen, A.P.,Stepanova, A.,Alonso, J.,Heber, S.,Malinowski, R.,Kirpekar, F.,Warren, A.J.,Helariutta, Y.
Recruitment of bifunctional regulator thermospermine to methylated ribosomes directs xylem fate.
Science, 391:694-699, 2026

PubMed Abstract: Polyamines are often associated with ribosomes and are thought to stabilize their integrity. In , the polyamine thermospermine (tSpm) affects xylem cell fate. tSpm induces translation of SUPPRESSOR-OF-ACAULIS51 (SAC51) and SAC51-LIKEs (SACLs), which inhibit heterodimerization of the xylem development proteins LONESOME-HIGHWAY (LHW) and TARGET-OF-MONOPTEROS5. Here, we report a methyltransferase, OVERACHIEVER, that methylates the peptidyl transferase center of the 25 ribosomal RNA (rRNA). Residue mU2952 promotes functional tSpm binding to a specific site connecting the P-site transfer RNA (tRNA) with rRNA residues in the peptidyl transferase center. This interaction enhances the translation of SACLs but inhibits that of LHW. Our study uncovers the dependency between a conserved rRNA base methylation and a polyamine in orchestrating cell fate decisions, highlighting a role for the ribosome chemical landscape in translational regulation.

PubMed: 41678627
DOI: 10.1126/science.adx2867

Experimental method

ELECTRON MICROSCOPY (1.82 Å)