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| - | ==Structural insights into cognate vs. near-cognate discrimination during decoding. This entry contains the small subunit of a ribosome programmed with a near-cognate codon, A/T-site tRNA, P-site tRNA, mRNA and EF-Tu==
| + | #REDIRECT [[4v6l]] This PDB entry is obsolete and replaced by 4v6l |
| - | <StructureSection load='3izv' size='340' side='right' caption='[[3izv]], [[Resolution|resolution]] 13.20Å' scene=''>
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| - | == Structural highlights ==
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| - | <table><tr><td colspan='2'>[[3izv]] is a 25 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli], [http://en.wikipedia.org/wiki/Escherichia_coli_dh1 Escherichia coli dh1], [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12] and [http://en.wikipedia.org/wiki/Escherichia_coli_o157:h7 Escherichia coli o157:h7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IZV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IZV FirstGlance]. <br>
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| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=3AU:3-[(3S)-3-AMINO-3-CARBOXYPROPYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>3AU</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</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=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=MIA:2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>MIA</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>
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| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3izt|3izt]]</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=3izv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3izv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3izv RCSB], [http://www.ebi.ac.uk/pdbsum/3izv PDBsum]</span></td></tr>
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| - | </table>
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| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | The structural basis of the tRNA selection process is investigated by cryo-electron microscopy of ribosomes programmed with UGA codons and incubated with ternary complex (TC) containing the near-cognate Trp-tRNA(Trp) in the presence of kirromycin. Going through more than 350 000 images and employing image classification procedures, we find approximately 8% in which the TC is bound to the ribosome. The reconstructed 3D map provides a means to characterize the arrangement of the near-cognate aa-tRNA with respect to elongation factor Tu (EF-Tu) and the ribosome, as well as the domain movements of the ribosome. One of the interesting findings is that near-cognate tRNA's acceptor stem region is flexible and CCA end becomes disordered. The data bring direct structural insights into the induced-fit mechanism of decoding by the ribosome, as the analysis of the interactions between small and large ribosomal subunit, aa-tRNA and EF-Tu and comparison with the cognate case (UGG codon) offers clues on how the conformational signals conveyed to the GTPase differ in the two cases.
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| - | Structural insights into cognate versus near-cognate discrimination during decoding.,Agirrezabala X, Schreiner E, Trabuco LG, Lei J, Ortiz-Meoz RF, Schulten K, Green R, Frank J EMBO J. 2011 Mar 4. PMID:21378755<ref>PMID:21378755</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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| - | ==See Also==
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| - | *[[Elongation factor|Elongation factor]]
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| - | *[[Ribosome 3D structures|Ribosome 3D structures]]
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| - | == References ==
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| - | <references/>
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| - | __TOC__
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| - | </StructureSection>
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| - | [[Category: Escherichia coli]]
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| - | [[Category: Escherichia coli dh1]]
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| - | [[Category: Escherichia coli k-12]]
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| - | [[Category: Escherichia coli o157:h7]]
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| - | [[Category: Agirrezabala, X]]
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| - | [[Category: Frank, J]]
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| - | [[Category: Green, R]]
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| - | [[Category: Lei, J]]
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| - | [[Category: Ortiz-Meoz, R F]]
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| - | [[Category: Schreiner, E]]
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| - | [[Category: Schulten, K]]
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| - | [[Category: Trabuco, L G]]
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| - | [[Category: Cryoem]]
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| - | [[Category: Near-cognate]]
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| - | [[Category: Ribosome]]
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| - | [[Category: Ternary complex]]
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| - | [[Category: Translation]]
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| - | [[Category: Trna incorporation]]
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