6H58
Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - Full 100S Hibernating E. coli Ribosome
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Summary for 6H58
| Entry DOI | 10.2210/pdb6h58/pdb |
| Related | 6H4N |
| EMDB information | 0137 0139 |
| Descriptor | 50S ribosomal protein L32, 50S ribosomal protein L3, 50S ribosomal protein L4, ... (56 entities in total) |
| Functional Keywords | 100s, cryo-em, e-site trna, hibernation, hpf, ribosome, rmf, s1 |
| Biological source | Escherichia coli BW25113 More |
| Total number of polymer chains | 112 |
| Total formula weight | 4434579.60 |
| Authors | Beckert, B.,Turk, M.,Czech, A.,Berninghausen, O.,Beckmann, R.,Ignatova, Z.,Plitzko, J.,Wilson, D.N. (deposition date: 2018-07-24, release date: 2018-09-05, Last modification date: 2024-10-09) |
| Primary citation | Beckert, B.,Turk, M.,Czech, A.,Berninghausen, O.,Beckmann, R.,Ignatova, Z.,Plitzko, J.M.,Wilson, D.N. Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1. Nat Microbiol, 3:1115-1121, 2018 Cited by PubMed Abstract: To survive under conditions of stress, such as nutrient deprivation, bacterial 70S ribosomes dimerize to form hibernating 100S particles. In γ-proteobacteria, such as Escherichia coli, 100S formation requires the ribosome modulation factor (RMF) and the hibernation promoting factor (HPF). Here we present single-particle cryo-electron microscopy structures of hibernating 70S and 100S particles isolated from stationary-phase E. coli cells at 3.0 Å and 7.9 Å resolution, respectively. The structures reveal the binding sites for HPF and RMF as well as the unexpected presence of deacylated E-site transfer RNA and ribosomal protein bS1. HPF interacts with the anticodon-stem-loop of the E-tRNA and occludes the binding site for the messenger RNA as well as A- and P-site tRNAs. RMF facilitates stabilization of a compact conformation of bS1, which together sequester the anti-Shine-Dalgarno sequence of the 16S ribosomal RNA (rRNA), thereby inhibiting translation initiation. At the dimerization interface, the C-terminus of uS2 probes the mRNA entrance channel of the symmetry-related particle, thus suggesting that dimerization inactivates ribosomes by blocking the binding of mRNA within the channel. The back-to-back E. coli 100S arrangement is distinct from 100S particles observed previously in Gram-positive bacteria, and reveals a unique role for bS1 in translation regulation. PubMed: 30177741DOI: 10.1038/s41564-018-0237-0 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (7.9 Å) |
Structure validation
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