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4gkk

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==Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a human mitochondrial anticodon stem loop (ASL) of transfer RNA Methionine (TRNAMET) bound to an mRNA with an AUA-codon in the A-site and paromomycin==
==Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a human mitochondrial anticodon stem loop (ASL) of transfer RNA Methionine (TRNAMET) bound to an mRNA with an AUA-codon in the A-site and paromomycin==
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<StructureSection load='4gkk' size='340' side='right' caption='[[4gkk]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
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<StructureSection load='4gkk' size='340' side='right'caption='[[4gkk]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4gkk]] is a 23 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GKK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GKK FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4gkk]] is a 10 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=4GKK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GKK FirstGlance]. <br>
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</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=PAR:PAROMOMYCIN'>PAR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.2&#8491;</td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=RSQ:5-FORMYLCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>RSQ</scene></td></tr>
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<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=PAR:PAROMOMYCIN'>PAR</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=RSQ:5-FORMYLCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>RSQ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3t1y|3t1y]], [[2kry|2kry]], [[2uuc|2uuc]]</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4gkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gkk OCA], [https://pdbe.org/4gkk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gkk RCSB], [https://www.ebi.ac.uk/pdbsum/4gkk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gkk ProSAT]</span></td></tr>
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<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=4gkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gkk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gkk RCSB], [http://www.ebi.ac.uk/pdbsum/4gkk PDBsum]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B]
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Codon use among the three domains of life is not confined to the universal genetic code. With only 22 tRNA genes in mammalian mitochondria, exceptions from the universal code are necessary for proper translation. A particularly interesting deviation is the decoding of the isoleucine AUA codon as methionine by the one mitochondrial-encoded tRNAMet. This tRNA decodes AUA and AUG in both the A- and P-sites of the metazoan mitochondrial ribosome. Enrichment of posttranscriptional modifications is a commonly appropriated mechanism for modulating decoding rules, enabling some tRNA functions while restraining others. In this case, a modification of cytidine, 5-formylcytidine (f5C), at the wobble position-34 of human mitochondrial () enables expanded decoding of AUA, resulting in a deviation in the genetic code. Visualization of the codon*anticodon interaction by X-ray crystallography revealed that recognition of both A and G at the third position of the codon occurs in the canonical Watson-Crick geometry. A modification-dependent shift in the tautomeric equilibrium toward the rare imino-oxo tautomer of cytidine stabilizes the f5C34*A base pair geometry with two hydrogen bonds.
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Expanded use of sense codons is regulated by modified cytidines in tRNA.,Cantara WA, Murphy FV 4th, Demirci H, Agris PF Proc Natl Acad Sci U S A. 2013 Jun 18. PMID:23781103<ref>PMID:23781103</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==See Also==
==See Also==
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*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
*[[Ribosome 3D structures|Ribosome 3D structures]]
*[[Ribosome 3D structures|Ribosome 3D structures]]
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== References ==
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*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Thermus thermophilus]]
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[[Category: Large Structures]]
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[[Category: Agris, P F]]
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[[Category: Thermus thermophilus HB8]]
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[[Category: Cantara, W A]]
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[[Category: Agris PF]]
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[[Category: Demirci, H]]
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[[Category: Cantara WA]]
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[[Category: IV, F V.Murphy]]
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[[Category: Demirci H]]
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[[Category: Spears, J L]]
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[[Category: Murphy IV FV]]
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[[Category: 5-formylcytidine]]
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[[Category: Spears JL]]
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[[Category: Ribosome-antibiotic complex]]
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[[Category: Translation initiation]]
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Current revision

Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a human mitochondrial anticodon stem loop (ASL) of transfer RNA Methionine (TRNAMET) bound to an mRNA with an AUA-codon in the A-site and paromomycin

PDB ID 4gkk

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