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| | <SX load='5zet' size='340' side='right' viewer='molstar' caption='[[5zet]], [[Resolution|resolution]] 3.20Å' scene=''> | | <SX load='5zet' size='340' side='right' viewer='molstar' caption='[[5zet]], [[Resolution|resolution]] 3.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5zet]] is a 34 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis_str._mc2_155 Mycobacterium smegmatis str. mc2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZET OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZET FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5zet]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZET OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZET FirstGlance]. <br> |
| - | </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5zet FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zet OCA], [http://pdbe.org/5zet PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zet RCSB], [http://www.ebi.ac.uk/pdbsum/5zet PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zet 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]] 3.2Å</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=5zet FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zet OCA], [https://pdbe.org/5zet PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zet RCSB], [https://www.ebi.ac.uk/pdbsum/5zet PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zet ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/A0QSG8_MYCS2 A0QSG8_MYCS2]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341][SAAS:SAAS00687840] [[http://www.uniprot.org/uniprot/I7GFB2_MYCS2 I7GFB2_MYCS2]] 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] [[http://www.uniprot.org/uniprot/RL10_MYCS2 RL10_MYCS2]] Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. [[http://www.uniprot.org/uniprot/RL3_MYCS2 RL3_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RL21_MYCS2 RL21_MYCS2]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363] [[http://www.uniprot.org/uniprot/RL2_MYCS2 RL2_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RL22_MYCS2 RL22_MYCS2]] 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).[HAMAP-Rule:MF_01331] 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.[HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/RL20_MYCS2 RL20_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RL9_MYCS2 RL9_MYCS2]] Binds to the 23S rRNA. [[http://www.uniprot.org/uniprot/RL31_MYCS2 RL31_MYCS2]] Binds the 23S rRNA. [[http://www.uniprot.org/uniprot/RL4_MYCS2 RL4_MYCS2]] 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.[HAMAP-Rule:MF_01328] Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_01328] [[http://www.uniprot.org/uniprot/RL13_MYCS2 RL13_MYCS2]] 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] [[http://www.uniprot.org/uniprot/RL16_MYCS2 RL16_MYCS2]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs. [[http://www.uniprot.org/uniprot/I7FGD9_MYCS2 I7FGD9_MYCS2]] 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] [[http://www.uniprot.org/uniprot/RL19_MYCS2 RL19_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RL24_MYCS2 RL24_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RL11_MYCS2 RL11_MYCS2]] Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors.[HAMAP-Rule:MF_00736] [[http://www.uniprot.org/uniprot/RL5_MYCS2 RL5_MYCS2]] 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.[HAMAP-Rule:MF_01333] [[http://www.uniprot.org/uniprot/RL14_MYCS2 RL14_MYCS2]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. [[http://www.uniprot.org/uniprot/RL23_MYCS2 RL23_MYCS2]] 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.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RL6_MYCS2 RL6_MYCS2]] 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. | + | [https://www.uniprot.org/uniprot/RL2_MYCS2 RL2_MYCS2] 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. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </SX> | | </SX> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Mycobacterium smegmatis str. mc2 155]] | + | [[Category: Mycolicibacterium smegmatis MC2 155]] |
| - | [[Category: Ahmed, T]] | + | [[Category: Ahmed T]] |
| - | [[Category: Bhushan, S]] | + | [[Category: Bhushan S]] |
| - | [[Category: Mishra, S]] | + | [[Category: Mishra S]] |
| - | [[Category: Shi, J]] | + | [[Category: Shi J]] |
| - | [[Category: Tyagi, A]] | + | [[Category: Tyagi A]] |
| - | [[Category: Complex]]
| + | |
| - | [[Category: Ribosome]]
| + | |
| - | [[Category: Translating-state]]
| + | |
| Structural highlights
Function
RL2_MYCS2 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.
Publication Abstract from PubMed
Ribosomes are the dynamic protein synthesis machineries of the cell. They may exist in different functional states in the cell. Therefore, it is essential to have structural information on these different functional states of ribosomes to understand their mechanism of action. Here, we present single particle cryo-EM reconstructions of the Mycobacterium smegmatis 70S ribosomes in the hibernating state (with HPF), trans-translating state (with tmRNA), and the P/P state (with P-tRNA) resolved to 4.1, 12.5, and 3.4 A, respectively. A comparison of the P/P state with the hibernating state provides possible functional insights about the Mycobacteria-specific helix H54a rRNA segment. Interestingly, densities for all the four OB domains of bS1 protein is visible in the hibernating 70S ribosome displaying the molecular details of bS1-70S interactions. Our structural data shows a Mycobacteria-specific H54a-bS1 interaction which seems to prevent subunit dissociation and degradation during hibernation without the formation of 100S dimer. This indicates a new role of bS1 protein in 70S protection during hibernation in Mycobacteria in addition to its conserved function during translation initiation.
Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA.,Mishra S, Ahmed T, Tyagi A, Shi J, Bhushan S Sci Rep. 2018 Sep 11;8(1):13587. doi: 10.1038/s41598-018-31850-3. PMID:30206241[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Mishra S, Ahmed T, Tyagi A, Shi J, Bhushan S. Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA. Sci Rep. 2018 Sep 11;8(1):13587. doi: 10.1038/s41598-018-31850-3. PMID:30206241 doi:http://dx.doi.org/10.1038/s41598-018-31850-3
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