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| {{Large structure}}
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| ==The complete structure of the Mycobacterium smegmatis 70S ribosome== | | ==The complete structure of the Mycobacterium smegmatis 70S ribosome== |
| <StructureSection load='5o61' size='340' side='right' caption='[[5o61]], [[Resolution|resolution]] 3.31Å' scene=''> | | <SX load='5o61' size='340' side='right' viewer='molstar' caption='[[5o61]], [[Resolution|resolution]] 3.31Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[5o61]] is a 57 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=5O61 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O61 FirstGlance]. <br> | | <table><tr><td colspan='2'>[[5o61]] 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=5O61 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O61 FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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]] 3.31Å</td></tr> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5o5j|5o5j]], [[5o60|5o60]]</td></tr>
| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5o61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o61 OCA], [http://pdbe.org/5o61 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o61 RCSB], [http://www.ebi.ac.uk/pdbsum/5o61 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o61 ProSAT]</span></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=5o61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o61 OCA], [https://pdbe.org/5o61 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o61 RCSB], [https://www.ebi.ac.uk/pdbsum/5o61 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o61 ProSAT]</span></td></tr> |
| </table> | | </table> |
| {{Large structure}}
| |
| == Function == | | == Function == |
| [[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/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/A0QSG5_MYCS2 A0QSG5_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/RS10_MYCS2 RS10_MYCS2]] Involved in the binding of tRNA to the ribosomes. [[http://www.uniprot.org/uniprot/A0A0D6J3X3_MYCSM A0A0D6J3X3_MYCSM]] Binds together with S18 to 16S ribosomal RNA.[HAMAP-Rule:MF_00360][SAAS:SAAS00348112] [[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/I7G436_MYCS2 I7G436_MYCS2]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341][SAAS:SAAS00687840] [[http://www.uniprot.org/uniprot/RS15_MYCS2 RS15_MYCS2]] 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] [[http://www.uniprot.org/uniprot/A0R3D2_MYCS2 A0R3D2_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/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/RS19_MYCS2 RS19_MYCS2]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA.[HAMAP-Rule:MF_00531] [[http://www.uniprot.org/uniprot/RS14Z_MYCS2 RS14Z_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RS8_MYCS2 RS8_MYCS2]] 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] [[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/RS12_MYCS2 RS12_MYCS2]] 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). [[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/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/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/RS5_MYCS2 RS5_MYCS2]] With S4 and S12 plays an important role in translational accuracy.[HAMAP-Rule:MF_01307] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body.[HAMAP-Rule:MF_01307] [[http://www.uniprot.org/uniprot/RS17_MYCS2 RS17_MYCS2]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RL9_MYCS2 RL9_MYCS2]] Binds to the 23S rRNA. [[http://www.uniprot.org/uniprot/RS7_MYCS2 RS7_MYCS2]] 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. [[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/RS13_MYCS2 RS13_MYCS2]] 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. [[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/RS182_MYCS2 RS182_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RS4_MYCS2 RS4_MYCS2]] 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. [[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. [[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/RL31_MYCS2 RL31_MYCS2]] Binds the 23S rRNA. [[http://www.uniprot.org/uniprot/RS11_MYCS2 RS11_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RS3_MYCS2 RS3_MYCS2]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. [[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/RS20_MYCS2 RS20_MYCS2]] Binds directly to 16S ribosomal RNA. [[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. | | [https://www.uniprot.org/uniprot/A0QTP4_MYCS2 A0QTP4_MYCS2] |
| <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| </div> | | </div> |
| <div class="pdbe-citations 5o61" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5o61" style="background-color:#fffaf0;"></div> |
| | |
| | ==See Also== |
| | *[[Ribosome 3D structures|Ribosome 3D structures]] |
| == References == | | == References == |
| <references/> | | <references/> |
| __TOC__ | | __TOC__ |
| </StructureSection> | | </SX> |
| [[Category: Mycobacterium smegmatis str. mc2 155]] | | [[Category: Large Structures]] |
| [[Category: Ban, N]] | | [[Category: Mycolicibacterium smegmatis MC2 155]] |
| [[Category: Boehringer, D]] | | [[Category: Ban N]] |
| [[Category: Burnside, C]] | | [[Category: Boehringer D]] |
| [[Category: Hentschel, J]] | | [[Category: Burnside C]] |
| [[Category: Leibundgut, M]] | | [[Category: Hentschel J]] |
| [[Category: Mignot, I]] | | [[Category: Leibundgut M]] |
| [[Category: Ribosome]]
| | [[Category: Mignot I]] |
| [[Category: Translation]]
| |