1ibl

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{{Seed}}
 
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[[Image:1ibl.png|left|200px]]
 
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==STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH A MESSENGER RNA FRAGMENT AND COGNATE TRANSFER RNA ANTICODON STEM-LOOP BOUND AT THE A SITE AND WITH THE ANTIBIOTIC PAROMOMYCIN==
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The line below this paragraph, containing "STRUCTURE_1ibl", creates the "Structure Box" on the page.
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<StructureSection load='1ibl' size='340' side='right'caption='[[1ibl]], [[Resolution|resolution]] 3.11&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1ibl]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. The February 2012 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoglycoside Antibiotics'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2012_2 10.2210/rcsb_pdb/mom_2012_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IBL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IBL FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 3.11&#8491;</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=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_1ibl| PDB=1ibl | SCENE= }}
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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=1ibl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ibl OCA], [https://pdbe.org/1ibl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ibl RCSB], [https://www.ebi.ac.uk/pdbsum/1ibl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ibl ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RS13_THET8 RS13_THET8] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome structure it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the top of the two subunits; these bridges are in contact with the A site and P site tRNAs respectively and are implicated in movement during ribosome translocation. Separately contacts the tRNAs in the A and P sites.[HAMAP-Rule:MF_01315]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ib/1ibl_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1ibl ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the antibiotic paromomycin, have been solved at between 3.1 and 3.3 angstroms resolution. Cognate transfer RNA (tRNA) binding induces global domain movements of the 30S subunit and changes in the conformation of the universally conserved and essential bases A1492, A1493, and G530 of 16S RNA. These bases interact intimately with the minor groove of the first two base pairs between the codon and anticodon, thus sensing Watson-Crick base-pairing geometry and discriminating against near-cognate tRNA. The third, or "wobble," position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs.
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===STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH A MESSENGER RNA FRAGMENT AND COGNATE TRANSFER RNA ANTICODON STEM-LOOP BOUND AT THE A SITE AND WITH THE ANTIBIOTIC PAROMOMYCIN===
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Recognition of cognate transfer RNA by the 30S ribosomal subunit.,Ogle JM, Brodersen DE, Clemons WM Jr, Tarry MJ, Carter AP, Ramakrishnan V Science. 2001 May 4;292(5518):897-902. PMID:11340196<ref>PMID:11340196</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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<div class="pdbe-citations 1ibl" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_11340196}}, adds the Publication Abstract to the page
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*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 11340196 is the PubMed ID number.
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*[[Ribosome 3D structures|Ribosome 3D structures]]
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== References ==
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{{ABSTRACT_PUBMED_11340196}}
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<references/>
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__TOC__
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==About this Structure==
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</StructureSection>
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1IBL is a [[Protein complex]] structure of sequences 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=1IBL OCA].
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[[Category: Aminoglycoside Antibiotics]]
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[[Category: Large Structures]]
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==Reference==
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[[Category: RCSB PDB Molecule of the Month]]
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Recognition of cognate transfer RNA by the 30S ribosomal subunit., Ogle JM, Brodersen DE, Clemons WM Jr, Tarry MJ, Carter AP, Ramakrishnan V, Science. 2001 May 4;292(5518):897-902. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11340196 11340196]
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[[Category: Protein complex]]
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[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
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[[Category: Brodersen, D E.]]
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[[Category: Brodersen DE]]
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[[Category: Carter, A P.]]
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[[Category: Carter AP]]
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[[Category: Jr., W M.Clemons.]]
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[[Category: Clemons Jr WM]]
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[[Category: Ogle, J M.]]
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[[Category: Ogle JM]]
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[[Category: Ramakrishnan, V.]]
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[[Category: Ramakrishnan V]]
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[[Category: Tarry, M J.]]
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[[Category: Tarry MJ]]
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[[Category: 30s ribosomal subunit]]
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[[Category: A site]]
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[[Category: Antibiotic]]
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[[Category: Anticodon]]
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[[Category: Codon]]
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[[Category: Decoding]]
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[[Category: Messenger rna]]
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[[Category: Mrna]]
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[[Category: Paromomycin]]
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[[Category: Ribosome]]
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[[Category: Stem-loop]]
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[[Category: Transfer rna]]
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[[Category: Trna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 10:43:11 2008''
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Current revision

STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH A MESSENGER RNA FRAGMENT AND COGNATE TRANSFER RNA ANTICODON STEM-LOOP BOUND AT THE A SITE AND WITH THE ANTIBIOTIC PAROMOMYCIN

PDB ID 1ibl

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