View source for 1qd3


==HIV-1 TAR RNA/NEOMYCIN B COMPLEX==
<StructureSection load='1qd3' size='340' side='right'caption='[[1qd3]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1qd3]] 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=1QD3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QD3 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=BDG:O-2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSE'>BDG</scene>, <scene name='pdbligand=CYY:2-DEOXYSTREPTAMINE'>CYY</scene>, <scene name='pdbligand=IDG:O-2,6-DIAMINO-2,6-DIDEOXY-BETA-L-IDOPYRANOSE'>IDG</scene>, <scene name='pdbligand=RIB:RIBOSE'>RIB</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=1qd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qd3 OCA], [https://pdbe.org/1qd3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qd3 RCSB], [https://www.ebi.ac.uk/pdbsum/1qd3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qd3 ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Binding of human immunodeficiency virus type 1 (HIV-1) transactivator (Tat) protein to Tat-responsive RNA (TAR) is essential for viral replication and is considered a promising starting point for the design of anti-HIV drugs. NMR spectroscopy indicated that the aminoglycosides neomycin B and ribostamycin bind to TAR and that neomycin is able to inhibit Tat binding to TAR. The solution structure of the neomycin-bound TAR has been determined by NMR spectroscopy. Chemical shift mapping and intermolecular nuclear Overhauser effects define the binding region of the aminoglycosides on TAR and give strong evidence for minor groove binding. Based on 15 nuclear Overhauser effect-derived intermolecular distance restraints, a model structure of the TAR-neomycin complex was calculated. Neomycin is bound in a binding pocket formed by the minor groove of the lower stem and the uridine-rich bulge of TAR, which adopts a conformation different from those known. The neamine core of the aminoglycoside (rings I and II) is covered with the bulge, explaining the inhibition of Tat by an allosteric mechanism. Neomycin reduces the volume of the major groove in which Tat is bound and thus impedes essential protein-RNA contacts.

Structural rearrangements of HIV-1 Tat-responsive RNA upon binding of neomycin B.,Faber C, Sticht H, Schweimer K, Rosch P J Biol Chem. 2000 Jul 7;275(27):20660-6. PMID:10747964<ref>PMID:10747964</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1qd3" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Human immunodeficiency virus 1]]
[[Category: Large Structures]]
[[Category: Faber C]]
[[Category: Roesch P]]
[[Category: Sticht H]]