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| <SX load='3iy8' size='340' side='right' viewer='molstar' caption='[[3iy8]], [[Resolution|resolution]] 14.10Å' scene=''> | | <SX load='3iy8' size='340' side='right' viewer='molstar' caption='[[3iy8]], [[Resolution|resolution]] 14.10Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[3iy8]] is a 11 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Leishmania_tarentolae Leishmania tarentolae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IY8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IY8 FirstGlance]. <br> | | <table><tr><td colspan='2'>[[3iy8]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Leishmania_tarentolae Leishmania tarentolae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IY8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IY8 FirstGlance]. <br> |
| </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=3iy8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iy8 OCA], [http://pdbe.org/3iy8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3iy8 RCSB], [http://www.ebi.ac.uk/pdbsum/3iy8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3iy8 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]] 14.1Å</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=3iy8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iy8 OCA], [https://pdbe.org/3iy8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iy8 RCSB], [https://www.ebi.ac.uk/pdbsum/3iy8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iy8 ProSAT]</span></td></tr> |
| </table> | | </table> |
| == Function == | | == Function == |
| [[http://www.uniprot.org/uniprot/RS11_ECOLI 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] [[http://www.uniprot.org/uniprot/RS18_ECOUT RS18_ECOUT]] 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 (By similarity). [[http://www.uniprot.org/uniprot/RS6_ECOLI RS6_ECOLI]] Binds together with S18 to 16S ribosomal RNA.[HAMAP-Rule:MF_00360] [[http://www.uniprot.org/uniprot/RS12_ECOLI 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] [[http://www.uniprot.org/uniprot/RS16_ECOLI RS16_ECOLI]] In addition to being a ribosomal protein, S16 also has a cation-dependent endonuclease activity.<ref>PMID:8730873</ref> 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.<ref>PMID:8730873</ref> [[http://www.uniprot.org/uniprot/RS5_ECOLI 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).<ref>PMID:15652481</ref> Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body.<ref>PMID:15652481</ref> 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.<ref>PMID:15652481</ref> [[http://www.uniprot.org/uniprot/RS15_ECO57 RS15_ECO57]] 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 (By similarity). Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS8_ECOLI 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] [[http://www.uniprot.org/uniprot/RS17_ECOLI 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] [[http://www.uniprot.org/uniprot/RS9_ECOLI 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.<ref>PMID:15308780</ref> | | [https://www.uniprot.org/uniprot/RS5_ECOLI 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).<ref>PMID:15652481</ref> Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body.<ref>PMID:15652481</ref> 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.<ref>PMID:15652481</ref> |
| == Evolutionary Conservation == | | == Evolutionary Conservation == |
| [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3iy8 ConSurf]. | | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3iy8 ConSurf]. |
| <div style="clear:both"></div> | | <div style="clear:both"></div> |
| <div style="background-color:#fffaf0;">
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| == Publication Abstract from PubMed ==
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| The Leishmania tarentolae mitochondrial ribosome (Lmr) is a minimal ribosomal RNA (rRNA)-containing ribosome. We have obtained a cryo-EM map of the Lmr. The map reveals several features that have not been seen in previously-determined structures of eubacterial or eukaryotic (cytoplasmic or organellar) ribosomes to our knowledge. Comparisons of the Lmr map with X-ray crystallographic and cryo-EM maps of the eubacterial ribosomes and a cryo-EM map of the mammalian mitochondrial ribosome show that (i) the overall structure of the Lmr is considerably more porous, (ii) the topology of the intersubunit space is significantly different, with fewer intersubunit bridges, but more tunnels, and (iii) several of the functionally-important rRNA regions, including the alpha-sarcin-ricin loop, have different relative positions within the structure. Furthermore, the major portions of the mRNA channel, the tRNA passage, and the nascent polypeptide exit tunnel contain Lmr-specific proteins, suggesting that the mechanisms for mRNA recruitment, tRNA interaction, and exiting of the nascent polypeptide in Lmr must differ markedly from the mechanisms deduced for ribosomes in other organisms. Our study identifies certain structural features that are characteristic solely of mitochondrial ribosomes and other features that are characteristic of both mitochondrial and chloroplast ribosomes (i.e., organellar ribosomes).
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| Structure of a mitochondrial ribosome with minimal RNA.,Sharma MR, Booth TM, Simpson L, Maslov DA, Agrawal RK Proc Natl Acad Sci U S A. 2009 Jun 16;106(24):9637-42. Epub 2009 Jun 3. PMID:19497863<ref>PMID:19497863</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 3iy8" style="background-color:#fffaf0;"></div>
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| ==See Also== | | ==See Also== |
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| *[[Ribosomal protein S8|Ribosomal protein S8]] | | *[[Ribosomal protein S8|Ribosomal protein S8]] |
| *[[Ribosomal protein S9|Ribosomal protein S9]] | | *[[Ribosomal protein S9|Ribosomal protein S9]] |
| | *[[Ribosome 3D structures|Ribosome 3D structures]] |
| == References == | | == References == |
| <references/> | | <references/> |
| __TOC__ | | __TOC__ |
| </SX> | | </SX> |
| [[Category: Escherichia coli]] | | [[Category: Escherichia coli K-12]] |
| [[Category: Large Structures]] | | [[Category: Large Structures]] |
| [[Category: Leishmania tarentolae]] | | [[Category: Leishmania tarentolae]] |
| [[Category: Agrawal, R K]] | | [[Category: Agrawal RK]] |
| [[Category: Booth, T M]] | | [[Category: Booth TM]] |
| [[Category: Maslov, D A]] | | [[Category: Maslov DA]] |
| [[Category: Sharma, M R]] | | [[Category: Sharma MR]] |
| [[Category: Simpson, L]] | | [[Category: Simpson L]] |
| [[Category: Antibiotic resistance]]
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| [[Category: Cryoem]]
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| [[Category: Endonuclease]]
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| [[Category: Hydrolase]]
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| [[Category: Methylation]]
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| [[Category: Minimal rna]]
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| [[Category: Mitochondrial ribosome]]
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| [[Category: Nuclease]]
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| [[Category: Repressor]]
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| [[Category: Ribonucleoprotein]]
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| [[Category: Ribosomal protein]]
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| [[Category: Ribosome]]
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| [[Category: Rna-binding]]
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| [[Category: Rrna-binding]]
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| [[Category: Translation regulation]]
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| [[Category: Trna-binding]]
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