6fxc

The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureusThe cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus

6fxc, resolution 6.76Å Show:Asymmetric Unit Biological Assembly Structural highlights 6fxc is a 104 chain structure with sequence from "micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885, Staab and Staphylococcus aureus. This structure supersedes the now removed PDB entry 5ng8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Experimental data: Check Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [RL16_STAAB] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs. [RL15_STAAB] Binds to the 23S rRNA. [A0A077VHU6_STAAU] 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.[HAMAP-Rule:MF_00480] [RL3_STAAB] 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_STAAB] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. [A0A1D4K9U8_STAAU] 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.[HAMAP-Rule:MF_00270] [RL13_STAAB] 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_STAAB] 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_STAAB] 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_STAAB] 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_STAAB] 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. [RS14Z_STAAB] 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] [RS20_STAAB] Binds directly to 16S ribosomal RNA. [RS10_STAAB] Involved in the binding of tRNA to the ribosomes. [RL14_STAAB] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. [W8TRE0_STAAU] 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.[HAMAP-Rule:MF_01337] [RS11_STAAB] 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. [A0A133Q8Z9_STAAU] 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:SAAS00720025] [HPF_STAAB] Required for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase; 100S ribosomes are translationally inactive and sometimes present during exponential growth. [RS13_STAAB] 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_STAAB] 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_STAAB] Binds together with S18 to 16S ribosomal RNA. [RL22_STAAB] 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. [RS3_STAAB] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. [RL19_STAAB] 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. [RL24_STAAB] 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. [A0A133PZQ5_STAAU] 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][RuleBase:RU003623] With S4 and S5 plays an important role in translational accuracy.[HAMAP-Rule:MF_00403][RuleBase:RU003623] [RS15_STAAB] 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. [RS8_STAAB] 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. [RL21_STAAB] This protein binds to 23S rRNA in the presence of protein L20. [RS4_STAAB] 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_STAAB] 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. [A0A133PYC3_STAAU] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA.[HAMAP-Rule:MF_00531] [RS5_STAAB] 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 PubMed Formation of 100S ribosome dimer is generally associated with translation suppression in bacteria. Trans-acting factors ribosome modulation factor (RMF) and hibernating promoting factor (HPF) were shown to directly mediate this process in E. coli. Gram-positive S. aureus lacks an RMF homolog and the structural basis for its 100S formation was not known. Here we report the cryo-electron microscopy structure of the native 100S ribosome from S. aureus, revealing the molecular mechanism of its formation. The structure is distinct from previously reported analogs and relies on the HPF C-terminal extension forming the binding platform for the interactions between both of the small ribosomal subunits. The 100S dimer is formed through interactions between rRNA h26, h40, and protein uS2, involving conformational changes of the head as well as surface regions that could potentially prevent RNA polymerase from docking to the ribosome.Under conditions of nutrient limitation, bacterial ribosomes undergo dimerization, forming a 100S complex that is translationally inactive. Here the authors present the structural basis for formation of the 100S complexes in Gram-positive bacteria, shedding light on the mechanism of translation suppression by the ribosome-silencing factors. The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus.,Matzov D, Aibara S, Basu A, Zimmerman E, Bashan A, Yap MF, Amunts A, Yonath AE Nat Commun. 2017 Sep 28;8(1):723. doi: 10.1038/s41467-017-00753-8. PMID:28959035 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Ribosome 3D structures