View source for 2ktz


==Inhibitor Induced Structural Change in the HCV IRES Domain IIa RNA==
<StructureSection load='2ktz' size='340' side='right'caption='[[2ktz]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2ktz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hepacivirus_C Hepacivirus C]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KTZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KTZ FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ISH:(7R)-7-[(DIMETHYLAMINO)METHYL]-1-[3-(DIMETHYLAMINO)PROPYL]-7,8-DIHYDRO-1H-FURO[3,2-E]BENZIMIDAZOL-2-AMINE'>ISH</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=2ktz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ktz OCA], [https://pdbe.org/2ktz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ktz RCSB], [https://www.ebi.ac.uk/pdbsum/2ktz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ktz ProSAT]</span></td></tr>
</table>
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== Publication Abstract from PubMed ==
Translation of the hepatitis C virus (HCV) RNA is initiated from a highly structured internal ribosomal entry site (IRES) in the 5' untranslated region (5' UTR) of the RNA genome. An important structural feature of the native RNA is an approximately 90 degrees helical bend localized to domain IIa that positions the apical loop of domain IIb of the IRES near the 40S ribosomal E-site to promote eIF2-GDP release, facilitating 80S ribosome assembly. We report here the NMR structure of a domain IIa construct in complex with a potent small-molecule inhibitor of HCV replication. Molecular dynamics refinement in explicit solvent and subsequent energetic analysis indicated that each inhibitor stereoisomer bound with comparable affinity and in an equivalent binding mode. The in silico analysis was substantiated by fluorescence-based assays showing that the relative binding free energies differed by only 0.7 kcal/mol. Binding of the inhibitor displaces key nucleotide residues within the bulge region, effecting a major conformational change that eliminates the bent RNA helical trajectory, providing a mechanism for the antiviral activity of this inhibitor class.

Inhibitor-induced structural change in the HCV IRES domain IIa RNA.,Paulsen RB, Seth PP, Swayze EE, Griffey RH, Skalicky JJ, Cheatham TE 3rd, Davis DR Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7263-8. Epub 2010 Apr 1. PMID:20360559<ref>PMID:20360559</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Hepacivirus C]]
[[Category: Large Structures]]
[[Category: Cheatham III TE]]
[[Category: Davis DR]]
[[Category: Griffey RH]]
[[Category: Paulsen RB]]
[[Category: Seth PP]]
[[Category: Skalicky JJ]]
[[Category: Swayze EE]]