1xpf

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spinqualitylabelsall models 1xpf, resolution 2.30Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

HIV-1 subtype A genomic RNA Dimerization Initiation Site

Overview

All retroviruses encapsidate their genome as a dimer of homologous, single-stranded RNAs. The dimerization initiation site (DIS) of human, immunodeficiency virus type 1 (HIV-1) is located in the 5'-untranslated, region of the viral genome and consists of a hairpin with a 6 nt, self-complementary loop sequence. Genomic RNA dimerization, a crucial step, for virion infectivity, is promoted by the formation of a loop-loop, complex (or kissing complex) between two DIS hairpins. Crystal structures, for the subtypes A, B and F of the HIV-1 DIS kissing complex have now been, solved at 2.3 A, 1.9 A and 1.6 A, respectively. They revealed a, polymorphism of bulged-out residues showing clearly that their, conformation is not a mere consequence of crystal packing. They also, provide more insights into ion binding, hydration, and RNA conformation, and flexibility. In particular, we observed the binding of spermine to the, loop-loop helix, which displaced a magnesium cation important for subtype, A DIS dimerization. The excellent agreement between X-ray structures and, the results of chemical probing and interference data on larger viral RNA, fragments shows that the crystal structures are relevant for the DIS, kissing complex present in solution and in viral particles. Accordingly, these structures will be helpful for designing new drugs derived from, aminoglycoside antibiotics and targeted against the RNA dimerization step, of the viral life-cycle.

About this Structure

1XPF is a Protein complex structure of sequences from [1] with SO4, MG, NA and SPM as ligands. Full crystallographic information is available from OCA.

Reference

Polymorphism of bulged-out residues in HIV-1 RNA DIS kissing complex and structure comparison with solution studies., Ennifar E, Dumas P, J Mol Biol. 2006 Feb 24;356(3):771-82. Epub 2005 Dec 21. PMID:16403527

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