2fcy
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 2fcy |SIZE=350|CAPTION= <scene name='initialview01'>2fcy</scene>, resolution 2.20Å | |PDB= 2fcy |SIZE=350|CAPTION= <scene name='initialview01'>2fcy</scene>, resolution 2.20Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=5BU:5-BROMO-URIDINE-5'-MONOPHOSPHATE'>5BU</scene>, <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NMY:NEOMYCIN'>NMY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2fcx|2FCX]], [[1xp7|1XP7]], [[1y3s|1Y3S]], [[1fcz|1FCZ]], [[2fd0|2FD0]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2fcy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fcy OCA], [http://www.ebi.ac.uk/pdbsum/2fcy PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2fcy RCSB]</span> | ||
}} | }} | ||
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[[Category: Marquet, R.]] | [[Category: Marquet, R.]] | ||
[[Category: Paillart, J C.]] | [[Category: Paillart, J C.]] | ||
| - | [[Category: CL]] | ||
| - | [[Category: K]] | ||
| - | [[Category: NMY]] | ||
| - | [[Category: SO4]] | ||
[[Category: aminoglycoside]] | [[Category: aminoglycoside]] | ||
[[Category: antibiotic]] | [[Category: antibiotic]] | ||
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[[Category: rna]] | [[Category: rna]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:01:07 2008'' |
Revision as of 00:01, 31 March 2008
| |||||||
| , resolution 2.20Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , , , | ||||||
| Related: | 2FCX, 1XP7, 1Y3S, 1FCZ, 2FD0
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
HIV-1 DIS kissing-loop in complex with Neomycin
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
2FCY 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 Mon Mar 31 03:01:07 2008
Categories: Protein complex | Dumas, P. | Ennifar, E. | Marquet, R. | Paillart, J C. | Aminoglycoside | Antibiotic | Hiv-1 | Rna
