1qd3
From Proteopedia
(New page: 200px<br /> <applet load="1qd3" size="450" color="white" frame="true" align="right" spinBox="true" caption="1qd3" /> '''HIV-1 TAR RNA/NEOMYCIN B COMPLEX'''<br /> ...) |
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| - | [[Image:1qd3.gif|left|200px]]<br /> | + | [[Image:1qd3.gif|left|200px]]<br /><applet load="1qd3" size="350" color="white" frame="true" align="right" spinBox="true" |
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'''HIV-1 TAR RNA/NEOMYCIN B COMPLEX'''<br /> | '''HIV-1 TAR RNA/NEOMYCIN B COMPLEX'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Binding of human immunodeficiency virus type 1 (HIV-1) transactivator | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 1QD3 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1] with BDG and CYY as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 1QD3 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1] with <scene name='pdbligand=BDG:'>BDG</scene> and <scene name='pdbligand=CYY:'>CYY</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QD3 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: nmr]] | [[Category: nmr]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:38:23 2008'' |
Revision as of 12:38, 21 February 2008
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HIV-1 TAR RNA/NEOMYCIN B COMPLEX
Overview
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.
About this Structure
1QD3 is a Protein complex structure of sequences from Human immunodeficiency virus 1 with and as ligands. Full crystallographic information is available from OCA.
Reference
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
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