5njt | pdb_00005njt
Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization.
Structural highlights
Function[RL16_BACSU] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs. [RS7_BACSU] 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] [RL5_BACSU] 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 (By similarity). [RS17_BACSU] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.[HAMAP-Rule:MF_01345] [RS18_BACSU] 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. [RL14_BACSU] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome (By similarity). [RL6_BACSU] 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 (By similarity). [RL4_BACSU] 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 (By similarity). Forms part of the polypeptide exit tunnel (By similarity). [RL10_BACSU] Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors (such as IF-2, EF-Tu, EF-G and RF3). [RL24_BACSU] 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 (By similarity).[1] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit (By similarity).[2] Has also been isolated as a basic, heat-shock stable DNA-binding protein from the B.subtilis nucleoid. It binds cooperatively to double-stranded supercoiled DNA which it further compacts into complexes 15-17 nm in diameter. Overexpression of the protein disrupts nucleoid segregation and positioning.[3] [RS14_BACSU] 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 (By similarity). The major S14 protein in the ribosome. Required for binding of S2 and S3 to the 30S subunit and for association of the 30S with the 50S subunit.[HAMAP-Rule:MF_01364] [RS20_BACSU] Binds directly to 16S ribosomal RNA. [RL3_BACSU] 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 (By similarity). Strongly stimulates 23S rRNA precursor processing by mini-ribonuclease 3 (MrnC); 20-30% DMSO can replace L3, suggesting the protein may alter rRNA conformation.[4] [RS10_BACSU] Involved in the binding of tRNA to the ribosomes. [RL15_BACSU] Binds to the 23S rRNA (By similarity). [RL19_BACSU] 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 (By similarity). [RS11_BACSU] 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. [RS13_BACSU] 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.[HAMAP-Rule:MF_01315] [RL2_BACSU] 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 (By similarity).[HAMAP-Rule:MF_01320] [RL13_BACSU] 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 (By similarity).[HAMAP-Rule:MF_01366] [RS6_BACSU] Binds together with S18 to 16S ribosomal RNA. [RL31_BACSU] Binds the 23S rRNA. While neither of the L31 paralogs is essential, this protein seems to function as the main L31 protein. Has a lower affinity for 70S ribosomes than the non-zinc-containing paralog L31B (ytiA); is displaced by it to varying extents, even under zinc-replete conditions. [RL23_BACSU] 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 (By similarity). [RS3_BACSU] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309] [RL20_BACSU] 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 (By similarity). [HPF_BACSU] Required for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase; 100S ribosomes are translationally inactive and sometimes present during exponential growth. May not be the only factor implicated (PubMed:22950019). Might negatively regulate the activity of the sigma-54 factor (SigL) (PubMed:9852014).[HAMAP-Rule:MF_00839][5] [6] [RL27_BACSU] Plays a role in sporulation at high temperatures.[7] [RS12_BACSU] With S4 and S5 plays an important role in translational accuracy. 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 (By similarity). [RS15_BACSU] 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.[HAMAP-Rule:MF_01343] Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343] [RS8_BACSU] 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.[HAMAP-Rule:MF_01302] [RL22_BACSU] 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 (By similarity). [RS4_BACSU] 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; many suppressors of streptomycin-dependent mutants of protein S12 are found in this protein, some but not all of which decrease translational accuracy (ram, ribosomal ambiguity mutations). S4 represses its own expression; it is not know if this is at the level of translation or of mRNA stability. [RL18_BACSU] 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 (By similarity).[8] Required for correct processing of both the 5' and 3' ends of 5S rRNA precursor, which is does in conjunction with ribonuclease M5 (RNase M5, rnmV). Possibly folds the 5S rRNA precursor into the correct conformation, thus acting as a chaperone.[9] [RL21_BACSU] This protein binds to 23S rRNA in the presence of protein L20 (By similarity). [RS19_BACSU] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. [RS5_BACSU] With S4 and S12 plays an important role in translational accuracy; many suppressors of streptomycin-dependent mutants of protein S12 are found in this protein, some but not all of which decrease translational accuracy (ram, ribosomal ambiguity mutations). Publication Abstract from PubMedUnder stress conditions, such as nutrient deprivation, bacteria enter into a hibernation stage, which is characterized by the appearance of 100S ribosomal particles. In Escherichia coli, dimerization of 70S ribosomes into 100S requires the action of the ribosome modulation factor (RMF) and the hibernation-promoting factor (HPF). Most other bacteria lack RMF and instead contain a long form HPF (LHPF), which is necessary and sufficient for 100S formation. While some structural information exists as to how RMF and HPF mediate formation of E. coli 100S (Ec100S), structural insight into 100S formation by LHPF has so far been lacking. Here we present a cryo-EM structure of the Bacillus subtilis hibernating 100S (Bs100S), revealing that the C-terminal domain (CTD) of the LHPF occupies a site on the 30S platform distinct from RMF Moreover, unlike RMF, the BsHPF-CTD is directly involved in forming the dimer interface, thereby illustrating the divergent mechanisms by which 100S formation is mediated in the majority of bacteria that contain LHPF, compared to some gamma-proteobacteria, such as E. coli. Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization.,Beckert B, Abdelshahid M, Schafer H, Steinchen W, Arenz S, Berninghausen O, Beckmann R, Bange G, Turgay K, Wilson DN EMBO J. 2017 Jul 14;36(14):2061-2072. doi: 10.15252/embj.201696189. Epub 2017 May, 3. PMID:28468753[10] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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