1XPE

HIV-1 subtype B genomic RNA Dimerization Initiation Site

Summary for 1XPE

• Entry DOI: 10.2210/pdb1xpe/pdb
• Related: 1JJM 1JJN 1K9W 1XP7 1XPF
• Descriptor: 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP*GP*CP*AP*AP*G)-3', MAGNESIUM ION, SODIUM ION, ... (6 entities in total)
• Functional Keywords: rna, loop-loop complex, hiv-1
• Total number of polymer chains: 2
• Total formula weight: 15395.25

Authors

Ennifar, E.,Dumas, P. (deposition date: 2004-10-08, release date: 2005-10-18, Last modification date: 2024-03-13)

Primary citation

Ennifar, E.,Dumas, P.
Polymorphism of Bulged-out Residues in HIV-1 RNA DIS Kissing Complex and Structure Comparison with Solution Studies
J.Mol.Biol., 356:771-782, 2006

PubMed Abstract: 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.

PubMed: 16403527
DOI: 10.1016/j.jmb.2005.12.022

Experimental method

X-RAY DIFFRACTION (1.94 Å)