1ond

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{{Seed}}
 
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[[Image:1ond.png|left|200px]]
 
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==THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TROLEANDOMYCIN MACROLIDE ANTIBIOTIC==
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The line below this paragraph, containing "STRUCTURE_1ond", creates the "Structure Box" on the page.
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<StructureSection load='1ond' size='340' side='right'caption='[[1ond]], [[Resolution|resolution]] 3.40&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'>[[1ond]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OND OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OND 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]] 3.4&#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=TAO:TROLEANDOMYCIN'>TAO</scene></td></tr>
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{{STRUCTURE_1ond| PDB=1ond | 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=1ond FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ond OCA], [https://pdbe.org/1ond PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ond RCSB], [https://www.ebi.ac.uk/pdbsum/1ond PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ond ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RL22_DEIRA RL22_DEIRA] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).[HAMAP-Rule:MF_01331_B] The globular domain of the protein is located by the polypeptide exit tunnel on the outside of the subunit while an extended beta-hairpin forms part of the wall of the tunnel. Forms a pair of "tweezers" with L32 that hold together two different domains of the 23S rRNA. Interacts with the tunnel-blocking modified macrolide azithromycin. Upon binding of the macrolide troleadomycin to the ribosome, the tip of the beta-hairpin is displaced, which severely restricts the tunnel. This and experiments in E.coli have led to the suggestion that it is part of the gating mechanism involved in translation arrest in the absence of the protein export system.[HAMAP-Rule:MF_01331_B]
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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/on/1ond_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1ond 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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Nascent proteins emerge out of ribosomes through an exit tunnel, which was assumed to be a firmly built passive path. Recent biochemical results, however, indicate that the tunnel plays an active role in sequence-specific gating of nascent chains and in responding to cellular signals. Consistently, modulation of the tunnel shape, caused by the binding of the semi-synthetic macrolide troleandomycin to the large ribosomal subunit from Deinococcus radiodurans, was revealed crystallographically. The results provide insights into the tunnel dynamics at high resolution. Here we show that, in addition to the typical steric blockage of the ribosomal tunnel by macrolides, troleandomycin induces a conformational rearrangement in a wall constituent, protein L22, flipping the tip of its highly conserved beta-hairpin across the tunnel. On the basis of mutations that alleviate elongation arrest, the tunnel motion could be correlated with sequence discrimination and gating, suggesting that specific arrest motifs within nascent chain sequences may induce a similar gating mechanism.
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===THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TROLEANDOMYCIN MACROLIDE ANTIBIOTIC===
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Structural insight into the role of the ribosomal tunnel in cellular regulation.,Berisio R, Schluenzen F, Harms J, Bashan A, Auerbach T, Baram D, Yonath A Nat Struct Biol. 2003 May;10(5):366-70. PMID:12665853<ref>PMID:12665853</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 1ond" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_12665853}}, adds the Publication Abstract to the page
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*[[Ribosomal protein L22|Ribosomal protein L22]]
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(as it appears on PubMed at http://www.pubmed.gov), where 12665853 is the PubMed ID number.
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*[[Ribosomal protein L32|Ribosomal protein L32]]
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== References ==
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{{ABSTRACT_PUBMED_12665853}}
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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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1OND is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OND OCA].
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==Reference==
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<ref group="xtra">PMID:12665853</ref><references group="xtra"/>
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[[Category: Deinococcus radiodurans]]
[[Category: Deinococcus radiodurans]]
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[[Category: Auerbach, T.]]
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[[Category: Large Structures]]
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[[Category: Baram, D.]]
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[[Category: Auerbach T]]
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[[Category: Bashan, A.]]
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[[Category: Baram D]]
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[[Category: Berisio, R.]]
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[[Category: Bashan A]]
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[[Category: Harms, J.]]
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[[Category: Berisio R]]
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[[Category: Schluenzen, F.]]
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[[Category: Harms J]]
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[[Category: Yonath, A.]]
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[[Category: Schluenzen F]]
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[[Category: Antibiotic]]
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[[Category: Yonath A]]
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[[Category: Blockage]]
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[[Category: Exit-tunnel l22]]
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[[Category: Macrolide]]
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[[Category: Ribosome]]
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[[Category: Trna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 21:23:55 2009''
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Current revision

THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TROLEANDOMYCIN MACROLIDE ANTIBIOTIC

PDB ID 1ond

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