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5el5
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 5el5 is ON HOLD Authors: Rozov, A., Demeshkina, N., Khusainov, I., Yusupov, M., Yusupova, G. Description: Structure of T. thermophilus 70S ribosome...) |
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| - | '''Unreleased structure''' | ||
| - | + | ==Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position== | |
| + | <StructureSection load='5el5' size='340' side='right'caption='[[5el5]], [[Resolution|resolution]] 3.15Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[5el5]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EL5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EL5 FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.15Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=T6A:N-[N-(9-B-D-RIBOFURANOSYLPURIN-6-YL)CARBAMOYL]THREONINE-5-MONOPHOSPHATE'>T6A</scene>, <scene name='pdbligand=U8U:5-METHYLAMINOMETHYL-2-THIOURIDINE-5-MONOPHOSPHATE'>U8U</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'>[https://proteopedia.org/fgij/fg.htm?mol=5el5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5el5 OCA], [https://pdbe.org/5el5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5el5 RCSB], [https://www.ebi.ac.uk/pdbsum/5el5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5el5 ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/RL14_THET8 RL14_THET8] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_01367] Contacts the 16S rRNA of the 30S subunit in two different positions helping to form bridges B5 and B8.[HAMAP-Rule:MF_01367] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNA(Lys)UUU with hypermodified 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine-pyrimidine mismatches. We show that mnm(5)s(2)U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism. | ||
| - | + | Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code.,Rozov A, Demeshkina N, Khusainov I, Westhof E, Yusupov M, Yusupova G Nat Commun. 2016 Jan 21;7:10457. doi: 10.1038/ncomms10457. PMID:26791911<ref>PMID:26791911</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: | + | <div class="pdbe-citations 5el5" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | |
| - | [[Category: | + | ==See Also== |
| - | [[Category: | + | *[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]] |
| - | [[Category: | + | *[[Ribosome 3D structures|Ribosome 3D structures]] |
| + | *[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Thermus thermophilus HB8]] | ||
| + | [[Category: Demeshkina N]] | ||
| + | [[Category: Khusainov I]] | ||
| + | [[Category: Rozov A]] | ||
| + | [[Category: Yusupov M]] | ||
| + | [[Category: Yusupova G]] | ||
Current revision
Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position
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