1M5L
Structure of wild-type and mutant internal loops from the SL-1 domain of the HIV-1 packaging signal
Summary for 1M5L
| Entry DOI | 10.2210/pdb1m5l/pdb |
| Descriptor | modified HIV-1 packaging signal stem-loop 1 RNA (1 entity in total) |
| Functional Keywords | base triplet, hiv, internal loop, packaging signal, sl-1, s-turn, rna |
| Total number of polymer chains | 1 |
| Total formula weight | 12381.42 |
| Authors | Gallego, J.,Greatorex, J.,Varani, G.,Lever, A. (deposition date: 2002-07-09, release date: 2002-09-18, Last modification date: 2024-05-22) |
| Primary citation | Greatorex, J.,Gallego, J.,Varani, G.,Lever, A. Structure and stability of wild-type and mutant RNA internal loops from the SL-1 domain of the HIV-1 packaging signal J.Mol.Biol., 322:543-557, 2002 Cited by PubMed Abstract: The packaging signal (Psi) of the human immunodeficiency virus type 1 (HIV-1) enables encapsidation of the full-length genomic RNA against a background of a vast excess of cellular mRNAs. The core HIV-1 Psi is approximately 109 nucleotides and contains sequences critical for viral genomic dimerisation and splicing, in addition to the packaging signal. It consists of a series of stem-loops (termed SL-1 to SL-4), which can be arranged in a cloverleaf secondary structure. Using a combination of NMR spectroscopy, UV melting experiments, molecular modeling and phylogenetic analyses, we have explored the structure of two conserved internal loops proximal to the palindromic sequence of SL-1. Internal loop A, composed of six purines, forms a flexible structure that is strikingly similar to the Rev responsive element motif when bound to Rev protein. This result suggests that it may function as a protein-binding site. The absolutely conserved four-purine internal loop B is instead conformationally and thermodynamically unstable, and exhibits multiple conformations in solution. By introducing a double AGG to GGA mutation within this loop, its conformation is stabilised to form a new intra-molecular G:A:G base-triplet. The structure of the GGA mutant explains the relative instability of the wild-type loop. In a manner analogous to SL-3, we propose that conformational flexibility at this site may facilitate melting of the structure during Gag protein capture or genomic RNA dimerisation. PubMed: 12225748DOI: 10.1016/S0022-2836(02)00776-3 PDB entries with the same primary citation |
| Experimental method | SOLUTION NMR |
Structure validation
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