6h58

Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - Full 100S Hibernating E. coli RibosomeStructure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - Full 100S Hibernating E. coli Ribosome

6h58, resolution 7.90Å

Structural highlights

6h58 is a 112 chain structure with sequence from Escherichia coli bw25113. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	6h4n
Experimental data:	Check
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RL19_ECOLI] This protein is located at the 30S-50S ribosomal subunit interface. In the 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit forming part of bridges B6 and B8. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA. The protein conformation is quite different between the 50S and 70S structures, which may be necessary for translocation.[HAMAP-Rule:MF_00402] [RL24_ECOLI] 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. It is not thought to be involved in the functions of the mature 50S subunit in vitro.^[1] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.^[2] [RL15_ECOLI] This protein binds the 5S rRNA. It is required for the late stages of subunit assembly, and is essential for 5S rRNA assembly onto the ribosome.[HAMAP-Rule:MF_01341_B] [RL16_ECOLI] This protein binds directly to 23S ribosomal RNA and is located at the A site of the peptidyltransferase center. It contacts the A and P site tRNAs. It has an essential role in subunit assembly, which is not well understood.[HAMAP-Rule:MF_01342] [RL29_ECOLI] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374] [RL14_ECOLI] This protein binds directly to 23S ribosomal RNA. In the E.coli 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit, forming part of bridges B5 and B8, connecting the 2 subunits. Although the protein undergoes significant rotation during the transition from an initiation to and EF-G bound state, the bridges remain stable. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA in bridges B5 and B8.^[3] Can also interact with RsfA, in this case bridge B8 probably cannot form, and the 30S and 50S ribosomal subunits do not associate, which represses translation.^[4] [RS13_ECOLI] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA.^[5] In the E.coli 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; bridge B1a is broken in the model with bound EF-G, while the protein-protein contacts between S13 and L5 in B1b change (PubMed:12809609). The 23S rRNA contact site in bridge B1a is modeled to differ in different ribosomal states (PubMed:16272117), contacting alternately S13 or S19. In the two 3.5 angstroms resolved ribosome structures (PubMed:12859903) the contacts between L5, S13 and S19 bridge B1b are different, confirming the dynamic nature of this interaction. Bridge B1a is not visible in the crystallized ribosomes due to 23S rRNA disorder.^[6] Contacts the tRNAs in the A and P sites.^[7] The C-terminal tail plays a role in the affinity of the 30S P site for different tRNAs.^[8] [RS1_ECOLI] Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence. [RL25_ECOLI] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Binds to the 5S rRNA independently of L5 and L18. Not required for binding of the 5S rRNA/L5/L18 subcomplex to 23S rRNA.[HAMAP-Rule:MF_01336] [RL23_ECOLI] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369] [RS9_ECOLI] The C-terminal tail plays a role in the affinity of the 30S P site for different tRNAs. Mutations that decrease this affinity are suppressed in the 70S ribosome.^[9] [RL9_ECOLI] One of the primary rRNA binding proteins, it binds very close to the 3' end of the 23S rRNA.[HAMAP-Rule:MF_00503] [RL18_ECOLI] This is one of the proteins that mediates the attachment of the 5S rRNA subcomplex onto the large ribosomal subunit where it forms part of the central protuberance. Binds stably to 5S rRNA; increases binding abilities of L5 in a cooperative fashion; both proteins together confer 23S rRNA binding. The 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.^[10] [RS18_ECOLI] 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] [RL22_ECOLI] 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.[HAMAP-Rule:MF_01331_B] The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome where it lines the wall of the exit tunnel. Removal of most of this hairpin (residues 85-95) does not prevent its incorporation into 70S ribosomes. Two of the hairpin residues (91 and 93) seem to be involved in translation elongation arrest of the SecM protein, as their replacement by larger amino acids alleviates the arrest.[HAMAP-Rule:MF_01331_B] [RL3_ECOLI] One of two assembly inititator proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325_B] [RS4_ECOLI] One of two assembly initiator proteins for the 30S subunit, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit.^[11] ^[12] ^[13] 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).^[14] ^[15] ^[16] Plays a role in mRNA unwinding by the ribosome, possibly by forming part of a processivity clamp.^[17] ^[18] ^[19] Protein S4 is also a translational repressor protein, it controls the translation of the alpha-operon (which codes for S13, S11, S4, RNA polymerase alpha subunit, and L17) by binding to its mRNA.^[20] ^[21] ^[22] Also functions as a rho-dependent antiterminator of rRNA transcription, increasing the synthesis of rRNA under conditions of excess protein, allowing a more rapid return to homeostasis. Binds directly to RNA polymerase.^[23] ^[24] ^[25] [RL4_ECOLI] 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.^[26] Protein L4 is a both a transcriptional repressor and a translational repressor protein; these two functions are independent of each other. It regulates transcription of the S10 operon (to which L4 belongs) by causing premature termination of transcription within the S10 leader; termination absolutely requires the NusA protein. L4 controls the translation of the S10 operon by binding to its mRNA. The regions of L4 that control regulation (residues 131-210) are different from those required for ribosome assembly (residues 89-103).^[27] Forms part of the polypeptide exit tunnel.^[28] Can regulate expression from Citrobacter freundii, Haemophilus influenzae, Morganella morganii, Salmonella typhimurium, Serratia marcescens, Vibrio cholerae and Yersinia enterocolitica (but not Pseudomonas aeruginosa) S10 leaders in vitro.^[29] [RMF_ECOLI] During stationary phase, converts 70S ribosomes to an inactive dimeric form (100S ribosomes). May form immature 90S particles, which are converted to mature 100S ribosomes by the hibernation promoting factor Hpf. Inactivates ribosomes by covering the peptidyl transferase (PTase) center of the 23S rRNA and the entrance of peptide exit tunnel. Also involved in protection against heat stress, but this role is not dependent on the maintenance of ribosome dimers.[HAMAP-Rule:MF_00919]^[30] ^[31] ^[32] ^[33] ^[34] ^[35] [RS17_ECOLI] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. Also plays a role in translational accuracy; neamine-resistant ribosomes show reduced neamine-induced misreading in vitro.[HAMAP-Rule:MF_01345] [RS11_ECOLI] 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 (By similarity).[HAMAP-Rule:MF_01310] [RL20_ECOLI] One of the primary rRNA binding proteins, it binds close to the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_00382] [RS15_ECOLI] 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] In the E.coli 70S ribosome it has been modeled (PubMed:12809609) to contact the 23S rRNA of the 50S subunit forming part of bridge B4. In the two 3.5 A resolved ribosome structures (PubMed:16272117) there are minor differences between side-chain conformations.[HAMAP-Rule:MF_01343] [RL6_ECOLI] This protein binds directly to at least 2 domains of the 23S ribosomal RNA, thus 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.[HAMAP-Rule:MF_01365] Gentamicin-resistant mutations in this protein affect translation fidelity.[HAMAP-Rule:MF_01365] [RL21_ECOLI] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363] [RL31_ECOLI] Binds the 23S rRNA (By similarity).[HAMAP-Rule:MF_00501] [RS19_ECOLI] In the E.coli 70S ribosome in the initiation state (PubMed:12809609) it has been modeled to contact the 23S rRNA of the 50S subunit forming part of bridge B1a; this bridge is broken in the model with bound EF-G. The 23S rRNA contact site in bridge B1a is modeled to differ in different ribosomal states (PubMed:12859903), contacting alternately S13 or S19. In the 3.5 angstroms resolved ribosome structures (PubMed:16272117) the contacts between L5, S13 and S19 bridge B1b are different, confirming the dynamic nature of this interaction. Bridge B1a is not visible in the crystallized ribosomes due to 23S rRNA disorder.[HAMAP-Rule:MF_00531] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. Contacts the A site tRNA.[HAMAP-Rule:MF_00531] [RS8_ECOLI] 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 (By similarity).[HAMAP-Rule:MF_01302_B] Protein S8 is a translational repressor protein, it controls the translation of the spc operon by binding to its mRNA.[HAMAP-Rule:MF_01302_B] [RS5_ECOLI] 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).^[36] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body.^[37] The physical location of this protein suggests it may also play a role in mRNA unwinding by the ribosome, possibly by forming part of a processivity clamp.^[38] [RL2_ECOLI] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. 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 highly controversial.[HAMAP-Rule:MF_01320_B] In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B] [RS20_ECOLI] Binds directly to 16S ribosomal RNA.[HAMAP-Rule:MF_00500] [RS10_ECOLI] Involved in the binding of tRNA to the ribosomes.[HAMAP-Rule:MF_00508] [RL5_ECOLI] 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. Its 5S rRNA binding is significantly enhanced in the presence of L18.[HAMAP-Rule:MF_01333_B] In the 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; the protein-protein contacts between S13 and L5 in B1b change in the model with bound EF-G implicating this bridge in subunit movement (PubMed:12809609 and PubMed:18723842). In the two 3.5 A resolved ribosome structures (PubMed:16272117) the contacts between L5, S13 and S19 are different, confirming the dynamic nature of this interaction.[HAMAP-Rule:MF_01333_B] Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333_B] [RS16_ECOLI] In addition to being a ribosomal protein, S16 also has a cation-dependent endonuclease activity.^[39] In-frame fusions with the ribosome maturation factor rimM suppress mutations in the latter (probably due to increased rimM expression) and are found in translationally active 70S ribosomes.^[40] [RL13_ECOLI] 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.[HAMAP-Rule:MF_01366] [RS7_ECOLI] 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, where it has been shown to contact mRNA. Has been shown to contact tRNA in both the P and E sites; it probably blocks exit of the E site tRNA.^[41] Protein S7 is also a translational repressor protein; it regulates the expression of the str operon members to different degrees by binding to its mRNA.^[42] [RS3_ECOLI] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation (By similarity).^[43] Plays a role in mRNA unwinding by the ribosome, possibly by forming part of a processivity clamp.^[44] [RS14_ECOLI] 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_00537] [RS6_ECOLI] Binds together with S18 to 16S ribosomal RNA.[HAMAP-Rule:MF_00360] [RS12_ECOLI] With S4 and S5 plays an important role in translational accuracy.[HAMAP-Rule:MF_00403_B] 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).[HAMAP-Rule:MF_00403_B] Cryo-EM studies suggest that S12 contacts the EF-Tu bound tRNA in the A-site during codon-recognition. This contact is most likely broken as the aminoacyl-tRNA moves into the peptidyl transferase center in the 50S subunit.[HAMAP-Rule:MF_00403_B] [RL17_ECOLI] Requires L15 for assembly into the 50S subunit.[HAMAP-Rule:MF_01368] [HPF_ECOLI] During stationary phase, promotes and stabilizes dimerization of 70S ribosomes by the ribosome modulation factor (RMF), leading to the formation of inactive 100S ribosomes. May convert immature 90S particles formed by RMF into 100S ribosomes. May also function as a potential translational inhibitor.^[45] ^[46] ^[47] ^[48]

Publication Abstract from PubMed

To survive under conditions of stress, such as nutrient deprivation, bacterial 70S ribosomes dimerize to form hibernating 100S particles(1). In gamma-proteobacteria, such as Escherichia coli, 100S formation requires the ribosome modulation factor (RMF) and the hibernation promoting factor (HPF)(2-4). 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 A and 7.9 A 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(5-8), and reveals a unique role for bS1 in translation regulation.

Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1.,Beckert B, Turk M, Czech A, Berninghausen O, Beckmann R, Ignatova Z, Plitzko JM, Wilson DN Nat Microbiol. 2018 Sep 3. pii: 10.1038/s41564-018-0237-0. doi:, 10.1038/s41564-018-0237-0. PMID:30177741^[49]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Spillmann S, Nierhaus KH. The ribosomal protein L24 of Escherichia coli is an assembly protein. J Biol Chem. 1978 Oct 10;253(19):7047-50. PMID:357435
↑ Spillmann S, Nierhaus KH. The ribosomal protein L24 of Escherichia coli is an assembly protein. J Biol Chem. 1978 Oct 10;253(19):7047-50. PMID:357435
↑ Hauser R, Pech M, Kijek J, Yamamoto H, Titz B, Naeve F, Tovchigrechko A, Yamamoto K, Szaflarski W, Takeuchi N, Stellberger T, Diefenbacher ME, Nierhaus KH, Uetz P. RsfA (YbeB) proteins are conserved ribosomal silencing factors. PLoS Genet. 2012;8(7):e1002815. doi: 10.1371/journal.pgen.1002815. Epub 2012 Jul , 19. PMID:22829778 doi:10.1371/journal.pgen.1002815
↑ Hauser R, Pech M, Kijek J, Yamamoto H, Titz B, Naeve F, Tovchigrechko A, Yamamoto K, Szaflarski W, Takeuchi N, Stellberger T, Diefenbacher ME, Nierhaus KH, Uetz P. RsfA (YbeB) proteins are conserved ribosomal silencing factors. PLoS Genet. 2012;8(7):e1002815. doi: 10.1371/journal.pgen.1002815. Epub 2012 Jul , 19. PMID:22829778 doi:10.1371/journal.pgen.1002815
↑ Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101
↑ Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101
↑ Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101
↑ Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101
↑ Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101
↑ Newberry V, Brosius J, Garrett R. Fragment of protein L18 from the Escherichia coli ribosome that contains the 5S RNA binding site. Nucleic Acids Res. 1978 Jun;5(6):1753-66. PMID:353728
↑ Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734
↑ Torres M, Condon C, Balada JM, Squires C, Squires CL. Ribosomal protein S4 is a transcription factor with properties remarkably similar to NusA, a protein involved in both non-ribosomal and ribosomal RNA antitermination. EMBO J. 2001 Jul 16;20(14):3811-20. PMID:11447122 doi:10.1093/emboj/20.14.3811
↑ Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042
↑ Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734
↑ Torres M, Condon C, Balada JM, Squires C, Squires CL. Ribosomal protein S4 is a transcription factor with properties remarkably similar to NusA, a protein involved in both non-ribosomal and ribosomal RNA antitermination. EMBO J. 2001 Jul 16;20(14):3811-20. PMID:11447122 doi:10.1093/emboj/20.14.3811
↑ Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042
↑ Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734
↑ Torres M, Condon C, Balada JM, Squires C, Squires CL. Ribosomal protein S4 is a transcription factor with properties remarkably similar to NusA, a protein involved in both non-ribosomal and ribosomal RNA antitermination. EMBO J. 2001 Jul 16;20(14):3811-20. PMID:11447122 doi:10.1093/emboj/20.14.3811
↑ Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042
↑ Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734
↑ Torres M, Condon C, Balada JM, Squires C, Squires CL. Ribosomal protein S4 is a transcription factor with properties remarkably similar to NusA, a protein involved in both non-ribosomal and ribosomal RNA antitermination. EMBO J. 2001 Jul 16;20(14):3811-20. PMID:11447122 doi:10.1093/emboj/20.14.3811
↑ Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042
↑ Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734
↑ Torres M, Condon C, Balada JM, Squires C, Squires CL. Ribosomal protein S4 is a transcription factor with properties remarkably similar to NusA, a protein involved in both non-ribosomal and ribosomal RNA antitermination. EMBO J. 2001 Jul 16;20(14):3811-20. PMID:11447122 doi:10.1093/emboj/20.14.3811
↑ Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042
↑ Freedman LP, Zengel JM, Archer RH, Lindahl L. Autogenous control of the S10 ribosomal protein operon of Escherichia coli: genetic dissection of transcriptional and posttranscriptional regulation. Proc Natl Acad Sci U S A. 1987 Sep;84(18):6516-20. PMID:2442760
↑ Freedman LP, Zengel JM, Archer RH, Lindahl L. Autogenous control of the S10 ribosomal protein operon of Escherichia coli: genetic dissection of transcriptional and posttranscriptional regulation. Proc Natl Acad Sci U S A. 1987 Sep;84(18):6516-20. PMID:2442760
↑ Freedman LP, Zengel JM, Archer RH, Lindahl L. Autogenous control of the S10 ribosomal protein operon of Escherichia coli: genetic dissection of transcriptional and posttranscriptional regulation. Proc Natl Acad Sci U S A. 1987 Sep;84(18):6516-20. PMID:2442760
↑ Freedman LP, Zengel JM, Archer RH, Lindahl L. Autogenous control of the S10 ribosomal protein operon of Escherichia coli: genetic dissection of transcriptional and posttranscriptional regulation. Proc Natl Acad Sci U S A. 1987 Sep;84(18):6516-20. PMID:2442760
↑ Yoshida H, Yamamoto H, Uchiumi T, Wada A. RMF inactivates ribosomes by covering the peptidyl transferase centre and entrance of peptide exit tunnel. Genes Cells. 2004 Apr;9(4):271-8. PMID:15066119 doi:http://dx.doi.org/10.1111/j.1356-9597.2004.00723.x
↑ Niven GW. Ribosome modulation factor protects Escherichia coli during heat stress, but this may not be dependent on ribosome dimerisation. Arch Microbiol. 2004 Sep;182(1):60-6. Epub 2004 Jul 20. PMID:15278243 doi:http://dx.doi.org/10.1007/s00203-004-0698-9
↑ Ueta M, Ohniwa RL, Yoshida H, Maki Y, Wada C, Wada A. Role of HPF (hibernation promoting factor) in translational activity in Escherichia coli. J Biochem. 2008 Mar;143(3):425-33. doi: 10.1093/jb/mvm243. Epub 2008 Jan 2. PMID:18174192 doi:http://dx.doi.org/10.1093/jb/mvm243
↑ Yoshida H, Ueta M, Maki Y, Sakai A, Wada A. Activities of Escherichia coli ribosomes in IF3 and RMF change to prepare 100S ribosome formation on entering the stationary growth phase. Genes Cells. 2009 Feb;14(2):271-80. doi: 10.1111/j.1365-2443.2008.01272.x. Epub, 2008 Jan 15. PMID:19170772 doi:http://dx.doi.org/10.1111/j.1365-2443.2008.01272.x
↑ Wada A, Igarashi K, Yoshimura S, Aimoto S, Ishihama A. Ribosome modulation factor: stationary growth phase-specific inhibitor of ribosome functions from Escherichia coli. Biochem Biophys Res Commun. 1995 Sep 14;214(2):410-7. PMID:7677746 doi:http://dx.doi.org/10.1006/bbrc.1995.2302
↑ Yamagishi M, Matsushima H, Wada A, Sakagami M, Fujita N, Ishihama A. Regulation of the Escherichia coli rmf gene encoding the ribosome modulation factor: growth phase- and growth rate-dependent control. EMBO J. 1993 Feb;12(2):625-30. PMID:8440252
↑ Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042
↑ Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042
↑ Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042
↑ Oberto J, Bonnefoy E, Mouray E, Pellegrini O, Wikstrom PM, Rouviere-Yaniv J. The Escherichia coli ribosomal protein S16 is an endonuclease. Mol Microbiol. 1996 Mar;19(6):1319-30. PMID:8730873
↑ Oberto J, Bonnefoy E, Mouray E, Pellegrini O, Wikstrom PM, Rouviere-Yaniv J. The Escherichia coli ribosomal protein S16 is an endonuclease. Mol Microbiol. 1996 Mar;19(6):1319-30. PMID:8730873
↑ Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734
↑ Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734
↑ Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042
↑ Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042
↑ Maki Y, Yoshida H, Wada A. Two proteins, YfiA and YhbH, associated with resting ribosomes in stationary phase Escherichia coli. Genes Cells. 2000 Dec;5(12):965-74. PMID:11168583
↑ Ueta M, Yoshida H, Wada C, Baba T, Mori H, Wada A. Ribosome binding proteins YhbH and YfiA have opposite functions during 100S formation in the stationary phase of Escherichia coli. Genes Cells. 2005 Dec;10(12):1103-12. PMID:16324148 doi:http://dx.doi.org/10.1111/j.1365-2443.2005.00903.x
↑ Ueta M, Ohniwa RL, Yoshida H, Maki Y, Wada C, Wada A. Role of HPF (hibernation promoting factor) in translational activity in Escherichia coli. J Biochem. 2008 Mar;143(3):425-33. doi: 10.1093/jb/mvm243. Epub 2008 Jan 2. PMID:18174192 doi:http://dx.doi.org/10.1093/jb/mvm243
↑ Yoshida H, Ueta M, Maki Y, Sakai A, Wada A. Activities of Escherichia coli ribosomes in IF3 and RMF change to prepare 100S ribosome formation on entering the stationary growth phase. Genes Cells. 2009 Feb;14(2):271-80. doi: 10.1111/j.1365-2443.2008.01272.x. Epub, 2008 Jan 15. PMID:19170772 doi:http://dx.doi.org/10.1111/j.1365-2443.2008.01272.x
↑ Beckert B, Turk M, Czech A, Berninghausen O, Beckmann R, Ignatova Z, Plitzko JM, Wilson DN. Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1. Nat Microbiol. 2018 Sep 3. pii: 10.1038/s41564-018-0237-0. doi:, 10.1038/s41564-018-0237-0. PMID:30177741 doi:http://dx.doi.org/10.1038/s41564-018-0237-0

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OCA

[1] Spillmann S, Nierhaus KH. The ribosomal protein L24 of Escherichia coli is an assembly protein. J Biol Chem. 1978 Oct 10;253(19):7047-50. PMID:357435

[2] Spillmann S, Nierhaus KH. The ribosomal protein L24 of Escherichia coli is an assembly protein. J Biol Chem. 1978 Oct 10;253(19):7047-50. PMID:357435

[3] Hauser R, Pech M, Kijek J, Yamamoto H, Titz B, Naeve F, Tovchigrechko A, Yamamoto K, Szaflarski W, Takeuchi N, Stellberger T, Diefenbacher ME, Nierhaus KH, Uetz P. RsfA (YbeB) proteins are conserved ribosomal silencing factors. PLoS Genet. 2012;8(7):e1002815. doi: 10.1371/journal.pgen.1002815. Epub 2012 Jul , 19. PMID:22829778 doi:10.1371/journal.pgen.1002815

[4] Hauser R, Pech M, Kijek J, Yamamoto H, Titz B, Naeve F, Tovchigrechko A, Yamamoto K, Szaflarski W, Takeuchi N, Stellberger T, Diefenbacher ME, Nierhaus KH, Uetz P. RsfA (YbeB) proteins are conserved ribosomal silencing factors. PLoS Genet. 2012;8(7):e1002815. doi: 10.1371/journal.pgen.1002815. Epub 2012 Jul , 19. PMID:22829778 doi:10.1371/journal.pgen.1002815

[5] Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101

[6] Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101

[7] Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101

[8] Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101

[9] Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101

[10] Newberry V, Brosius J, Garrett R. Fragment of protein L18 from the Escherichia coli ribosome that contains the 5S RNA binding site. Nucleic Acids Res. 1978 Jun;5(6):1753-66. PMID:353728

[11] Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734

[12] Torres M, Condon C, Balada JM, Squires C, Squires CL. Ribosomal protein S4 is a transcription factor with properties remarkably similar to NusA, a protein involved in both non-ribosomal and ribosomal RNA antitermination. EMBO J. 2001 Jul 16;20(14):3811-20. PMID:11447122 doi:10.1093/emboj/20.14.3811

[13] Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042

[14] Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734

[15] Torres M, Condon C, Balada JM, Squires C, Squires CL. Ribosomal protein S4 is a transcription factor with properties remarkably similar to NusA, a protein involved in both non-ribosomal and ribosomal RNA antitermination. EMBO J. 2001 Jul 16;20(14):3811-20. PMID:11447122 doi:10.1093/emboj/20.14.3811

[16] Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042

[17] Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734

[18] Torres M, Condon C, Balada JM, Squires C, Squires CL. Ribosomal protein S4 is a transcription factor with properties remarkably similar to NusA, a protein involved in both non-ribosomal and ribosomal RNA antitermination. EMBO J. 2001 Jul 16;20(14):3811-20. PMID:11447122 doi:10.1093/emboj/20.14.3811

[19] Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042

[20] Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734

[21] Torres M, Condon C, Balada JM, Squires C, Squires CL. Ribosomal protein S4 is a transcription factor with properties remarkably similar to NusA, a protein involved in both non-ribosomal and ribosomal RNA antitermination. EMBO J. 2001 Jul 16;20(14):3811-20. PMID:11447122 doi:10.1093/emboj/20.14.3811

[22] Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042

[23] Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734

[24] Torres M, Condon C, Balada JM, Squires C, Squires CL. Ribosomal protein S4 is a transcription factor with properties remarkably similar to NusA, a protein involved in both non-ribosomal and ribosomal RNA antitermination. EMBO J. 2001 Jul 16;20(14):3811-20. PMID:11447122 doi:10.1093/emboj/20.14.3811

[25] Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042

[26] Freedman LP, Zengel JM, Archer RH, Lindahl L. Autogenous control of the S10 ribosomal protein operon of Escherichia coli: genetic dissection of transcriptional and posttranscriptional regulation. Proc Natl Acad Sci U S A. 1987 Sep;84(18):6516-20. PMID:2442760

[27] Freedman LP, Zengel JM, Archer RH, Lindahl L. Autogenous control of the S10 ribosomal protein operon of Escherichia coli: genetic dissection of transcriptional and posttranscriptional regulation. Proc Natl Acad Sci U S A. 1987 Sep;84(18):6516-20. PMID:2442760

[28] Freedman LP, Zengel JM, Archer RH, Lindahl L. Autogenous control of the S10 ribosomal protein operon of Escherichia coli: genetic dissection of transcriptional and posttranscriptional regulation. Proc Natl Acad Sci U S A. 1987 Sep;84(18):6516-20. PMID:2442760

[29] Freedman LP, Zengel JM, Archer RH, Lindahl L. Autogenous control of the S10 ribosomal protein operon of Escherichia coli: genetic dissection of transcriptional and posttranscriptional regulation. Proc Natl Acad Sci U S A. 1987 Sep;84(18):6516-20. PMID:2442760

[30] Yoshida H, Yamamoto H, Uchiumi T, Wada A. RMF inactivates ribosomes by covering the peptidyl transferase centre and entrance of peptide exit tunnel. Genes Cells. 2004 Apr;9(4):271-8. PMID:15066119 doi:http://dx.doi.org/10.1111/j.1356-9597.2004.00723.x

[31] Niven GW. Ribosome modulation factor protects Escherichia coli during heat stress, but this may not be dependent on ribosome dimerisation. Arch Microbiol. 2004 Sep;182(1):60-6. Epub 2004 Jul 20. PMID:15278243 doi:http://dx.doi.org/10.1007/s00203-004-0698-9

[32] Ueta M, Ohniwa RL, Yoshida H, Maki Y, Wada C, Wada A. Role of HPF (hibernation promoting factor) in translational activity in Escherichia coli. J Biochem. 2008 Mar;143(3):425-33. doi: 10.1093/jb/mvm243. Epub 2008 Jan 2. PMID:18174192 doi:http://dx.doi.org/10.1093/jb/mvm243

[33] Yoshida H, Ueta M, Maki Y, Sakai A, Wada A. Activities of Escherichia coli ribosomes in IF3 and RMF change to prepare 100S ribosome formation on entering the stationary growth phase. Genes Cells. 2009 Feb;14(2):271-80. doi: 10.1111/j.1365-2443.2008.01272.x. Epub, 2008 Jan 15. PMID:19170772 doi:http://dx.doi.org/10.1111/j.1365-2443.2008.01272.x

[34] Wada A, Igarashi K, Yoshimura S, Aimoto S, Ishihama A. Ribosome modulation factor: stationary growth phase-specific inhibitor of ribosome functions from Escherichia coli. Biochem Biophys Res Commun. 1995 Sep 14;214(2):410-7. PMID:7677746 doi:http://dx.doi.org/10.1006/bbrc.1995.2302

[35] Yamagishi M, Matsushima H, Wada A, Sakagami M, Fujita N, Ishihama A. Regulation of the Escherichia coli rmf gene encoding the ribosome modulation factor: growth phase- and growth rate-dependent control. EMBO J. 1993 Feb;12(2):625-30. PMID:8440252

[36] Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042

[37] Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042

[38] Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042

[39] Oberto J, Bonnefoy E, Mouray E, Pellegrini O, Wikstrom PM, Rouviere-Yaniv J. The Escherichia coli ribosomal protein S16 is an endonuclease. Mol Microbiol. 1996 Mar;19(6):1319-30. PMID:8730873

[40] Oberto J, Bonnefoy E, Mouray E, Pellegrini O, Wikstrom PM, Rouviere-Yaniv J. The Escherichia coli ribosomal protein S16 is an endonuclease. Mol Microbiol. 1996 Mar;19(6):1319-30. PMID:8730873

[41] Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734

[42] Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734

[43] Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042

[44] Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042

[45] Maki Y, Yoshida H, Wada A. Two proteins, YfiA and YhbH, associated with resting ribosomes in stationary phase Escherichia coli. Genes Cells. 2000 Dec;5(12):965-74. PMID:11168583

[46] Ueta M, Yoshida H, Wada C, Baba T, Mori H, Wada A. Ribosome binding proteins YhbH and YfiA have opposite functions during 100S formation in the stationary phase of Escherichia coli. Genes Cells. 2005 Dec;10(12):1103-12. PMID:16324148 doi:http://dx.doi.org/10.1111/j.1365-2443.2005.00903.x

[47] Ueta M, Ohniwa RL, Yoshida H, Maki Y, Wada C, Wada A. Role of HPF (hibernation promoting factor) in translational activity in Escherichia coli. J Biochem. 2008 Mar;143(3):425-33. doi: 10.1093/jb/mvm243. Epub 2008 Jan 2. PMID:18174192 doi:http://dx.doi.org/10.1093/jb/mvm243

[48] Yoshida H, Ueta M, Maki Y, Sakai A, Wada A. Activities of Escherichia coli ribosomes in IF3 and RMF change to prepare 100S ribosome formation on entering the stationary growth phase. Genes Cells. 2009 Feb;14(2):271-80. doi: 10.1111/j.1365-2443.2008.01272.x. Epub, 2008 Jan 15. PMID:19170772 doi:http://dx.doi.org/10.1111/j.1365-2443.2008.01272.x

[49] Beckert B, Turk M, Czech A, Berninghausen O, Beckmann R, Ignatova Z, Plitzko JM, Wilson DN. Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1. Nat Microbiol. 2018 Sep 3. pii: 10.1038/s41564-018-0237-0. doi:, 10.1038/s41564-018-0237-0. PMID:30177741 doi:http://dx.doi.org/10.1038/s41564-018-0237-0

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[4]

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[7]

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[14]

[15]

[16]

[17]

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[19]

[20]

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[31]

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[34]

[35]

[36]

[37]

[38]

[39]

[40]

[41]

[42]

[43]

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[46]

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[48]

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6h58

Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - Full 100S Hibernating E. coli RibosomeStructure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - Full 100S Hibernating E. coli Ribosome

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6h58

Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - Full 100S Hibernating E. coli RibosomeStructure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - Full 100S Hibernating E. coli Ribosome

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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