5nd9 | pdb_00005nd9
Hibernating ribosome from Staphylococcus aureus (Rotated state)
Structural highlights
Function[RL16_STAA8] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs. [RL15_STAA8] Binds to the 23S rRNA. [RS7_STAA8] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. [RL3_STAA8] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. [RS17_STAA8] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. [RS18_STAA8] Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit. [RL13_STAA8] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly. [RL4_STAA8] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome. Forms part of the polypeptide exit tunnel. [RL2_STAA8] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. [RL5_STAA8] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. [RL23_STAA8] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome. [RS20_STAA8] Binds directly to 16S ribosomal RNA. [RS14Z_STAA8] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site.[HAMAP-Rule:MF_01364] [RS10_STAAM] Involved in the binding of tRNA to the ribosomes. [RL14_STAA8] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. [RL18_STAA8] This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. [RS11_STAA8] Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome. [Q2G0S0_STAA8] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.[HAMAP-Rule:MF_01334][SAAS:SAAS00023350] [HPF_STAA8] Required for dimerization of active 70S ribosomes into 100S ribosomes; when added to monomeric 70S ribosomes stimulates formation of 100S dimeric ribosomes. Unlike E.coli, 100S ribosomes are present during exponential growth, peak during early stationary phase and then decrease (shown for strain NBRC 3060).[HAMAP-Rule:MF_00839][1] [RS13_STAA8] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. [RL6_STAA8] This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. [RS6_STAA8] Binds together with S18 to 16S ribosomal RNA. [RL22_STAA8] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome. [RL19_STAA8] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. [RS3_STAA8] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. [RL24_STAA8] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. [RS12_STAA8] With S4 and S5 plays an important role in translational accuracy.[HAMAP-Rule:MF_00403] Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_00403] [RS15_STAA8] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome. [RL21_STAA8] This protein binds to 23S rRNA in the presence of protein L20. [RS8_STAA8] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit. [RS4_STAA8] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. [RL20_STAA8] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. [RS19_STAA8] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. [RS5_STAA8] With S4 and S12 plays an important role in translational accuracy. Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Publication Abstract from PubMedIn 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 Staphylococcus aureus 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. Structures and dynamics of hibernating ribosomes from Staphylococcus aureus mediated by intermolecular interactions of HPF.,Khusainov I, Vicens Q, Ayupov R, Usachev K, Myasnikov A, Simonetti A, Validov S, Kieffer B, Yusupova G, Yusupov M, Hashem Y EMBO J. 2017 Jul 14;36(14):2073-2087. doi: 10.15252/embj.201696105. Epub 2017 Jun, 23. PMID:28645916[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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