2l94
From Proteopedia
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==Structure of the HIV-1 frameshift site RNA bound to a small molecule inhibitor of viral replication== | ==Structure of the HIV-1 frameshift site RNA bound to a small molecule inhibitor of viral replication== | ||
| - | <StructureSection load='2l94' size='340' side='right' caption='[[2l94 | + | <StructureSection load='2l94' size='340' side='right'caption='[[2l94]]' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | [[2l94]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L94 OCA]. <br> | + | <table><tr><td colspan='2'>[[2l94]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L94 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2L94 FirstGlance]. <br> |
| - | <b>[[Ligand|Ligands:]]</b> <scene name='pdbligand=L94:N-{(Z)-AMINO[4-(AMINO{[3-(DIMETHYLAMMONIO)PROPYL]IMINIO}METHYL)PHENYL]METHYLIDENE}-N,N-DIMETHYLPROPANE-1,3-DIAMINIUM'>L94</scene>< | + | </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=L94:N-{(Z)-AMINO[4-(AMINO{[3-(DIMETHYLAMMONIO)PROPYL]IMINIO}METHYL)PHENYL]METHYLIDENE}-N,N-DIMETHYLPROPANE-1,3-DIAMINIUM'>L94</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=2l94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l94 OCA], [https://pdbe.org/2l94 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2l94 RCSB], [https://www.ebi.ac.uk/pdbsum/2l94 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2l94 ProSAT]</span></td></tr> |
| - | <b>Resources:</b> <span class='plainlinks'>[ | + | </table> |
| + | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
Programmed -1 translational frameshifting is an essential event in the replication cycle of HIV. Frameshifting is required for expression of the viral Pol proteins, and drug-like molecules that target this process may inhibit HIV replication. A small molecule stimulator of HIV-1 frameshifting and inhibitor of viral replication, DB213 (RG501), was previously discovered from a high-throughput screen. However, the mechanistic basis for this compound's effects was unknown, and to date no structural information exists for small molecule effectors of frameshifting. Here, we investigate the binding of DB213 to the frameshift site RNA and have determined the structure of this complex by NMR. Binding of DB213 stabilizes the RNA and increases its melting temperature by 10 degrees C. The ligand binds to a primary site on the RNA stem-loop, although nonspecific interactions are also detected. The compound binds in the major groove and spans a distance of 9 base pairs. DB213 hydrogen bonds to phosphate groups on opposite sides of the major groove and alters the conformation of a conserved GGA bulge in the RNA. This study may provide a starting point for structure-based optimization of compounds targeting the HIV-1 frameshift site RNA. | Programmed -1 translational frameshifting is an essential event in the replication cycle of HIV. Frameshifting is required for expression of the viral Pol proteins, and drug-like molecules that target this process may inhibit HIV replication. A small molecule stimulator of HIV-1 frameshifting and inhibitor of viral replication, DB213 (RG501), was previously discovered from a high-throughput screen. However, the mechanistic basis for this compound's effects was unknown, and to date no structural information exists for small molecule effectors of frameshifting. Here, we investigate the binding of DB213 to the frameshift site RNA and have determined the structure of this complex by NMR. Binding of DB213 stabilizes the RNA and increases its melting temperature by 10 degrees C. The ligand binds to a primary site on the RNA stem-loop, although nonspecific interactions are also detected. The compound binds in the major groove and spans a distance of 9 base pairs. DB213 hydrogen bonds to phosphate groups on opposite sides of the major groove and alters the conformation of a conserved GGA bulge in the RNA. This study may provide a starting point for structure-based optimization of compounds targeting the HIV-1 frameshift site RNA. | ||
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Structure of the HIV-1 Frameshift Site RNA Bound to a Small Molecule Inhibitor of Viral Replication.,Marcheschi RJ, Tonelli M, Kumar A, Butcher SE ACS Chem Biol. 2011 Aug 19;6(8):857-64. Epub 2011 Jun 15. PMID:21648432<ref>PMID:21648432</ref> | Structure of the HIV-1 Frameshift Site RNA Bound to a Small Molecule Inhibitor of Viral Replication.,Marcheschi RJ, Tonelli M, Kumar A, Butcher SE ACS Chem Biol. 2011 Aug 19;6(8):857-64. Epub 2011 Jun 15. PMID:21648432<ref>PMID:21648432</ref> | ||
| - | From | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| + | </div> | ||
| + | <div class="pdbe-citations 2l94" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Human immunodeficiency virus 1]] |
| - | [[Category: | + | [[Category: Large Structures]] |
| - | [[Category: | + | [[Category: Butcher SE]] |
| - | [[Category: | + | [[Category: Kumar A]] |
| - | [[Category: | + | [[Category: Marcheschi RJ]] |
| - | [[Category: | + | [[Category: Tonelli M]] |
| - | + | ||
Current revision
Structure of the HIV-1 frameshift site RNA bound to a small molecule inhibitor of viral replication
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