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| <SX load='3j9w' size='340' side='right' viewer='molstar' caption='[[3j9w]], [[Resolution|resolution]] 3.90Å' scene=''> | | <SX load='3j9w' size='340' side='right' viewer='molstar' caption='[[3j9w]], [[Resolution|resolution]] 3.90Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[3j9w]] is a 54 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J9W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J9W FirstGlance]. <br> | | <table><tr><td colspan='2'>[[3j9w]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J9W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J9W FirstGlance]. <br> |
| </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3j9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j9w OCA], [https://pdbe.org/3j9w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j9w RCSB], [https://www.ebi.ac.uk/pdbsum/3j9w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j9w ProSAT]</span></td></tr> | | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.9Å</td></tr> |
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3j9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j9w OCA], [https://pdbe.org/3j9w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j9w RCSB], [https://www.ebi.ac.uk/pdbsum/3j9w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j9w ProSAT]</span></td></tr> |
| </table> | | </table> |
| == Function == | | == Function == |
| [[https://www.uniprot.org/uniprot/RS7_BACSU 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] [[https://www.uniprot.org/uniprot/RS17_BACSU RS17_BACSU]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.[HAMAP-Rule:MF_01345] [[https://www.uniprot.org/uniprot/RS18_BACSU 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. [[https://www.uniprot.org/uniprot/RL15_BACSU RL15_BACSU]] Binds to the 23S rRNA (By similarity). [[https://www.uniprot.org/uniprot/RL31_BACSU 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. [[https://www.uniprot.org/uniprot/RL10_BACSU 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). [[https://www.uniprot.org/uniprot/RS14_BACSU 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] [[https://www.uniprot.org/uniprot/RS20_BACSU RS20_BACSU]] Binds directly to 16S ribosomal RNA. [[https://www.uniprot.org/uniprot/RL20_BACSU 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). [[https://www.uniprot.org/uniprot/RS10_BACSU RS10_BACSU]] Involved in the binding of tRNA to the ribosomes. [[https://www.uniprot.org/uniprot/RL2_BACSU 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] [[https://www.uniprot.org/uniprot/RS11_BACSU 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. [[https://www.uniprot.org/uniprot/RL24_BACSU 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).<ref>PMID:11278078</ref> One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit (By similarity).<ref>PMID:11278078</ref> 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.<ref>PMID:11278078</ref> [[https://www.uniprot.org/uniprot/RL19_BACSU 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). [[https://www.uniprot.org/uniprot/RL13_BACSU 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] [[https://www.uniprot.org/uniprot/RS13_BACSU 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] [[https://www.uniprot.org/uniprot/MIFM_BACSU MIFM_BACSU]] Sensor protein that upregulates translation of the secondary membrane protein insertase (MisCB/YqjG) when activity of the primary membrane protein insertase (MisCA/SpoIIIJ) is limited. Acts as a ribosome-nascent chain complex. When the primary membrane protein insertase activity or level is reduced, the membrane insertion of MifM is impaired, which induces arrest of MifM translation and unfolding of the mRNA hairpin. Unfolding leads to translation of the downstream gene, which encodes the secondary membrane protein insertase MisCB/YqjG. Translation arrest of MifM is mediated by interaction of its C-terminal domain with the ribosomal polypeptide exit tunnel. Undergoes multisite stalling, which may allow a sufficient duration of ribosomal stalling and consequently sufficient levels of MisCB/YqjG.<ref>PMID:19779460</ref> <ref>PMID:21383133</ref> <ref>PMID:22864117</ref> [[https://www.uniprot.org/uniprot/RS6_BACSU RS6_BACSU]] Binds together with S18 to 16S ribosomal RNA. [[https://www.uniprot.org/uniprot/RL21_BACSU RL21_BACSU]] This protein binds to 23S rRNA in the presence of protein L20 (By similarity). [[https://www.uniprot.org/uniprot/RL6_BACSU 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). [[https://www.uniprot.org/uniprot/RS3_BACSU 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] [[https://www.uniprot.org/uniprot/RL3_BACSU 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.<ref>PMID:19154332</ref> [[https://www.uniprot.org/uniprot/RL22_BACSU 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). [[https://www.uniprot.org/uniprot/RL11_BACSU RL11_BACSU]] This protein binds directly to 23S ribosomal RNA (By similarity). [[https://www.uniprot.org/uniprot/RS12_BACSU 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). [[https://www.uniprot.org/uniprot/RL18_BACSU 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).<ref>PMID:6432797</ref> 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.<ref>PMID:6432797</ref> [[https://www.uniprot.org/uniprot/RS15_BACSU 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] [[https://www.uniprot.org/uniprot/RS8_BACSU 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] [[https://www.uniprot.org/uniprot/RL23_BACSU 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). [[https://www.uniprot.org/uniprot/RL5_BACSU 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). [[https://www.uniprot.org/uniprot/RS4_BACSU 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. [[https://www.uniprot.org/uniprot/RL16_BACSU RL16_BACSU]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs. [[https://www.uniprot.org/uniprot/RL4_BACSU 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). [[https://www.uniprot.org/uniprot/RL14_BACSU RL14_BACSU]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome (By similarity). [[https://www.uniprot.org/uniprot/RS19_BACSU RS19_BACSU]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. [[https://www.uniprot.org/uniprot/RL27_BACSU RL27_BACSU]] Plays a role in sporulation at high temperatures.<ref>PMID:14586115</ref> [[https://www.uniprot.org/uniprot/RS5_BACSU 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).
| | [https://www.uniprot.org/uniprot/RS2_BACSU RS2_BACSU] |
| <div style="background-color:#fffaf0;">
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| == Publication Abstract from PubMed ==
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| Ribosomal stalling is used to regulate gene expression and can occur in a species-specific manner. Stalling during translation of the MifM leader peptide regulates expression of the downstream membrane protein biogenesis factor YidC2 (YqjG) in Bacillus subtilis, but not in Escherichia coli. In the absence of structures of Gram-positive bacterial ribosomes, a molecular basis for species-specific stalling has remained unclear. Here we present the structure of a Gram-positive B. subtilis MifM-stalled 70S ribosome at 3.5-3.9 A, revealing a network of interactions between MifM and the ribosomal tunnel, which stabilize a non-productive conformation of the PTC that prevents aminoacyl-tRNA accommodation and thereby induces translational arrest. Complementary genetic analyses identify a single amino acid within ribosomal protein L22 that dictates the species specificity of the stalling event. Such insights expand our understanding of how the synergism between the ribosome and the nascent chain is utilized to modulate the translatome in a species-specific manner.
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| | |
| Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling.,Sohmen D, Chiba S, Shimokawa-Chiba N, Innis CA, Berninghausen O, Beckmann R, Ito K, Wilson DN Nat Commun. 2015 Apr 23;6:6941. doi: 10.1038/ncomms7941. PMID:25903689<ref>PMID:25903689</ref>
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| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 3j9w" style="background-color:#fffaf0;"></div>
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| ==See Also== | | ==See Also== |
| | *[[Ribosome 3D structures|Ribosome 3D structures]] |
| *[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] | | *[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] |
| == References ==
| |
| <references/>
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| __TOC__ | | __TOC__ |
| </SX> | | </SX> |
| [[Category: Bacillus subtilis subsp. subtilis str. 168]] | | [[Category: Bacillus subtilis subsp. subtilis str. 168]] |
| [[Category: Large Structures]] | | [[Category: Large Structures]] |
| [[Category: Beckmann, R]] | | [[Category: Beckmann R]] |
| [[Category: Berninghausen, O]] | | [[Category: Berninghausen O]] |
| [[Category: Chiba, S]] | | [[Category: Chiba S]] |
| [[Category: Innis, C A]] | | [[Category: Innis CA]] |
| [[Category: Ito, K]] | | [[Category: Ito K]] |
| [[Category: Shimokawa-Chiba, N]] | | [[Category: Shimokawa-Chiba N]] |
| [[Category: Sohmen, D]] | | [[Category: Sohmen D]] |
| [[Category: Wilson, D N]] | | [[Category: Wilson DN]] |
| [[Category: L22]]
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| [[Category: Mifm]]
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| [[Category: Ribosome]]
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| [[Category: Stalling]]
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| [[Category: Translation arrest]]
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