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2fd0
From Proteopedia
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| - | [[Image:2fd0.gif|left|200px]] | + | [[Image:2fd0.gif|left|200px]] |
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| - | '''HIV-1 DIS kissing-loop in complex with lividomycin''' | + | {{Structure |
| + | |PDB= 2fd0 |SIZE=350|CAPTION= <scene name='initialview01'>2fd0</scene>, resolution 1.80Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=LIV:(2R,3S,4S,5S,6R)-2-((2S,3S,4R,5R,6R)-5-AMINO-2-(AMINOMETHYL)-6-((2R,3S,4R,5S)-5-((1R,2R,3S,5R,6S)-3,5-DIAMINO-2-((2S,3R,5S,6R)-3-AMINO-5-HYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-6-HYDROXYCYCLOHEXYLOXY)-4-HYDROXY-2-(HYDROXYMETHYL)-TETRAHYDROFURAN-3-YLOXY)-4-HYDROXY-TETRAHYDRO-2H-PYRAN-3-YLOXY)-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-3,4,5-TRIOL'>LIV</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene> and <scene name='pdbligand=CL:CHLORIDE ION'>CL</scene> | ||
| + | |ACTIVITY= | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''HIV-1 DIS kissing-loop in complex with lividomycin''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2FD0 is a [ | + | 2FD0 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FD0 OCA]. |
==Reference== | ==Reference== | ||
| - | Targeting the dimerization initiation site of HIV-1 RNA with aminoglycosides: from crystal to cell., Ennifar E, Paillart JC, Bodlenner A, Walter P, Weibel JM, Aubertin AM, Pale P, Dumas P, Marquet R, Nucleic Acids Res. 2006 May 5;34(8):2328-39. Print 2006. PMID:[http:// | + | Targeting the dimerization initiation site of HIV-1 RNA with aminoglycosides: from crystal to cell., Ennifar E, Paillart JC, Bodlenner A, Walter P, Weibel JM, Aubertin AM, Pale P, Dumas P, Marquet R, Nucleic Acids Res. 2006 May 5;34(8):2328-39. Print 2006. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16679451 16679451] |
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Dumas, P.]] | [[Category: Dumas, P.]] | ||
| Line 20: | Line 29: | ||
[[Category: LIV]] | [[Category: LIV]] | ||
[[Category: aminoglycoside]] | [[Category: aminoglycoside]] | ||
| - | [[Category: | + | [[Category: antibiotic]] |
[[Category: hiv-1]] | [[Category: hiv-1]] | ||
[[Category: rna]] | [[Category: rna]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:50:56 2008'' |
Revision as of 14:50, 20 March 2008
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| , resolution 1.80Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , and | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
HIV-1 DIS kissing-loop in complex with lividomycin
Overview
The kissing-loop complex that initiates dimerization of genomic RNA is crucial for Human Immunodeficiency Virus Type 1 (HIV-1) replication. We showed that owing to its strong similitude with the bacterial ribosomal A site it can be targeted by aminoglycosides. Here, we present its crystal structure in complex with neamine, ribostamycin, neomycin and lividomycin. These structures explain the specificity for 4,5-disubstituted 2-deoxystreptamine (DOS) derivatives and for subtype A and subtype F kissing-loop complexes, and provide a strong basis for rational drug design. As a consequence of the different topologies of the kissing-loop complex and the A site, these aminoglycosides establish more contacts with HIV-1 RNA than with 16S RNA. Together with biochemical experiments, they showed that while rings I, II and III confer binding specificity, rings IV and V are important for affinity. Binding of neomycin, paromomycin and lividomycin strongly stabilized the kissing-loop complex by bridging the two HIV-1 RNA molecules. Furthermore, in situ footprinting showed that the dimerization initiation site (DIS) of HIV-1 genomic RNA could be targeted by these aminoglycosides in infected cells and virions, demonstrating its accessibility.
About this Structure
2FD0 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Targeting the dimerization initiation site of HIV-1 RNA with aminoglycosides: from crystal to cell., Ennifar E, Paillart JC, Bodlenner A, Walter P, Weibel JM, Aubertin AM, Pale P, Dumas P, Marquet R, Nucleic Acids Res. 2006 May 5;34(8):2328-39. Print 2006. PMID:16679451
Page seeded by OCA on Thu Mar 20 16:50:56 2008
Categories: Protein complex | Dumas, P. | Ennifar, E. | Marquet, R. | Paillart, J C. | CL | K | LIV | Aminoglycoside | Antibiotic | Hiv-1 | Rna
