2uxc: Difference between revisions

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-[[Image:2uxc.png|left|200px]]
-{{STRUCTURE_2uxc|  PDB=2uxc  |  SCENE=  }}
+==Crystal structure of an extended tRNA anticodon stem loop in complex with its cognate mRNA UCGU in the context of the Thermus thermophilus 30S subunit.==
+<StructureSection load='2uxc' size='340' side='right'caption='[[2uxc]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2uxc]] 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=2UXC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2UXC 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]] 2.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <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>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2uxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2uxc OCA], [https://pdbe.org/2uxc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2uxc RCSB], [https://www.ebi.ac.uk/pdbsum/2uxc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2uxc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[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]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ux/2uxc_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=2uxc ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+During translation, some +1 frameshift mRNA sites are decoded by frameshift suppressor tRNAs that contain an extra base in their anticodon loops. Similarly engineered tRNAs have been used to insert nonnatural amino acids into proteins. Here, we report crystal structures of two anticodon stem-loops (ASLs) from tRNAs known to facilitate +1 frameshifting bound to the 30S ribosomal subunit with their cognate mRNAs. ASL(CCCG) and ASL(ACCC) (5'-3' nomenclature) form unpredicted anticodon-codon interactions where the anticodon base 34 at the wobble position contacts either the fourth codon base or the third and fourth codon bases. In addition, we report the structure of ASL(ACGA) bound to the 30S ribosomal subunit with its cognate mRNA. The tRNA containing this ASL was previously shown to be unable to facilitate +1 frameshifting in competition with normal tRNAs (Hohsaka et al. 2001), and interestingly, it displays a normal anticodon-codon interaction. These structures show that the expanded anticodon loop of +1 frameshift promoting tRNAs are flexible enough to adopt conformations that allow three bases of the anticodon to span four bases of the mRNA. Therefore it appears that normal triplet pairing is not an absolute constraint of the decoding center.
-===CRYSTAL STRUCTURE OF AN EXTENDED TRNA ANTICODON STEM LOOP IN COMPLEX WITH ITS COGNATE MRNA UCGU IN THE CONTEXT OF THE THERMUS THERMOPHILUS 30S SUBUNIT.===
+Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit.,Dunham CM, Selmer M, Phelps SS, Kelley AC, Suzuki T, Joseph S, Ramakrishnan V RNA. 2007 Jun;13(6):817-23. Epub 2007 Apr 6. PMID:17416634<ref>PMID:17416634</ref>
-{{ABSTRACT_PUBMED_17416634}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2uxc" style="background-color:#fffaf0;"></div>
-[[2uxc]] is a 23 chain structure of [[Ribosomal protein S10]], [[Ribosomal protein S11]], [[Ribosomal protein S12]], [[Ribosomal protein S13]], [[Ribosomal protein S14]], [[Ribosomal protein S15]], [[Ribosomal protein S16]], [[Ribosomal protein S17]], [[Ribosomal protein S18]], [[Ribosomal protein S19]], [[Ribosomal protein S2]], [[Ribosomal protein S20]], [[Ribosomal protein S3]], [[Ribosomal protein S4]], [[Ribosomal protein S5]], [[Ribosomal protein S6]], [[Ribosomal protein S7]], [[Ribosomal protein S8]], [[Ribosomal protein S9]], [[Ribosomal protein THX]] and [[Ribosome]] 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=2UXC OCA].
 ==See Also==
-*[[Ribosomal protein S10|Ribosomal protein S10]]
+*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
-*[[Ribosomal protein S11|Ribosomal protein S11]]
+*[[Ribosome 3D structures|Ribosome 3D structures]]
-*[[Ribosomal protein S12|Ribosomal protein S12]]
+== References ==
-*[[Ribosomal protein S13|Ribosomal protein S13]]
+<references/>
-*[[Ribosomal protein S14|Ribosomal protein S14]]
+__TOC__
-*[[Ribosomal protein S15|Ribosomal protein S15]]
+</StructureSection>
-*[[Ribosomal protein S16|Ribosomal protein S16]]
+[[Category: Large Structures]]
-*[[Ribosomal protein S17|Ribosomal protein S17]]
+[[Category: Thermus thermophilus HB8]]
-*[[Ribosomal protein S18|Ribosomal protein S18]]
+[[Category: Dunham CM]]
-*[[Ribosomal protein S19|Ribosomal protein S19]]
+[[Category: Joseph S]]
-*[[Ribosomal protein S2|Ribosomal protein S2]]
+[[Category: Kelley AC]]
-*[[Ribosomal protein S20|Ribosomal protein S20]]
+[[Category: Phelps SS]]
-*[[Ribosomal protein S3|Ribosomal protein S3]]
+[[Category: Ramakrishnan V]]
-*[[Ribosomal protein S4|Ribosomal protein S4]]
+[[Category: Selmer M]]
-*[[Ribosomal protein S5|Ribosomal protein S5]]
+[[Category: Suzuki T]]
-*[[Ribosomal protein S6|Ribosomal protein S6]]
-*[[Ribosomal protein S7|Ribosomal protein S7]]
-*[[Ribosomal protein S8|Ribosomal protein S8]]
-*[[Ribosomal protein S9|Ribosomal protein S9]]
-*[[Ribosomal protein THX|Ribosomal protein THX]]
-*[[Ribosome|Ribosome]]
-==Reference==
-<ref group="xtra">PMID:017416634</ref><references group="xtra"/>
-[[Category: Thermus thermophilus]]
-[[Category: Dunham, C M.]]
-[[Category: Joseph, S.]]
-[[Category: Kelley, A C.]]
-[[Category: Phelps, S S.]]
-[[Category: Ramakrishnan, V.]]
-[[Category: Selmer, M.]]
-[[Category: Suzuki, T.]]
-[[Category: 30s ribosomal subunit]]
-[[Category: A site]]
-[[Category: Anticodon]]
-[[Category: Codon]]
-[[Category: Decoding]]
-[[Category: Frameshift]]
-[[Category: Frameshift suppressor trna]]
-[[Category: Messenger rna]]
-[[Category: Metal-binding]]
-[[Category: Mrna]]
-[[Category: Paromomycin]]
-[[Category: Ribonucleoprotein]]
-[[Category: Ribosomal protein]]
-[[Category: Ribosome]]
-[[Category: Rna-binding]]
-[[Category: Rrna-binding]]
-[[Category: Stem-loop]]
-[[Category: Transfer rna]]
-[[Category: Trna]]
-[[Category: Trna-binding]]
-[[Category: Zinc-finger]]