5ND8
Hibernating ribosome from Staphylococcus aureus (Unrotated state)
This is a non-PDB format compatible entry.
Summary for 5ND8
| Entry DOI | 10.2210/pdb5nd8/pdb |
| EMDB information | 3624 |
| Descriptor | 16S ribosomal RNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... (52 entities in total) |
| Functional Keywords | s.aureus, hpf, hibernation, 100s ribosome, ribosome |
| Biological source | Staphylococcus aureus (strain NCTC 8325) More |
| Total number of polymer chains | 52 |
| Total formula weight | 2160703.53 |
| Authors | Khusainov, I.,Vicens, Q.,Ayupov, R.,Usachev, K.,Myasnikov, A.,Simonetti, A.,Validov, S.,Kieffer, B.,Yusupova, G.,Yusupov, M.,Hashem, Y. (deposition date: 2017-03-07, release date: 2017-06-28, Last modification date: 2024-05-15) |
| Primary citation | Khusainov, I.,Vicens, Q.,Ayupov, R.,Usachev, K.,Myasnikov, A.,Simonetti, A.,Validov, S.,Kieffer, B.,Yusupova, G.,Yusupov, M.,Hashem, Y. Structures and dynamics of hibernating ribosomes from Staphylococcus aureus mediated by intermolecular interactions of HPF. EMBO J., 36:2073-2087, 2017 Cited by PubMed Abstract: In bacteria, ribosomal hibernation shuts down translation as a response to stress, through reversible binding of stress-induced proteins to ribosomes. This process typically involves the formation of 100S ribosome dimers. Here, we present the structures of hibernating ribosomes from human pathogen containing a long variant of the hibernation-promoting factor (SaHPF) that we solved using cryo-electron microscopy. Our reconstructions reveal that the N-terminal domain (NTD) of SaHPF binds to the 30S subunit as observed for shorter variants of HPF in other species. The C-terminal domain (CTD) of SaHPF protrudes out of each ribosome in order to mediate dimerization. Using NMR, we characterized the interactions at the CTD-dimer interface. Secondary interactions are provided by helix 26 of the 16S ribosomal RNA We also show that ribosomes in the 100S particle adopt both rotated and unrotated conformations. Overall, our work illustrates a specific mode of ribosome dimerization by long HPF, a finding that may help improve the selectivity of antimicrobials. PubMed: 28645916DOI: 10.15252/embj.201696105 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.7 Å) |
Structure validation
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