2LDL | pdb_00002ldl

Solution NMR Structure of the HIV-1 Exon Splicing Silencer 3

PDB DOI: https://doi.org/10.2210/pdb2LDL/pdb
BMRB: 17671
NAKB: 2LDL

Classification: RNA
Organism(s): Human immunodeficiency virus 1
Mutation(s): No

Deposited: 2011-05-27 Released: 2011-12-28
Deposition Author(s): Mishler, C., Levengood, J.D., Johnson, C.A., Rajan, P., Znosko, B.M.

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 256
Conformers Submitted: 12
Selection Criteria: structures with the lowest energy

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Solution Structure of the HIV-1 Exon Splicing Silencer 3.

Levengood, J.D., Rollins, C., Mishler, C.H., Johnson, C.A., Miner, G., Rajan, P., Znosko, B.M., Tolbert, B.S.

(2012) J Mol Biology 415: 680-698

PubMed: 22154809 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2011.11.034
Primary Citation Related Structures:
2LDL

PubMed Abstract:
Alternative splicing of the human immunodeficiency virus type 1 (HIV-1) genomic RNA is necessary to produce the complete viral protein complement, and aberrations in the splicing pattern impair HIV-1 replication. Genome splicing in HIV-1 is tightly regulated by the dynamic assembly/disassembly of trans host factors with cis RNA control elements. The host protein, heterogeneous nuclear ribonucleoprotein (hnRNP) A1, regulates splicing at several highly conserved HIV-1 3' splice sites by binding 5'-UAG-3' elements embedded within regions containing RNA structure. The physical determinants of hnRNP A1 splice site recognition remain poorly defined in HIV-1, thus precluding a detailed understanding of the molecular basis of the splicing pattern. Here, the three-dimensional structure of the exon splicing silencer 3 (ESS3) from HIV-1 has been determined using NMR spectroscopy. ESS3 adopts a 27-nucleotide hairpin with a 10-bp A-form stem that contains a pH-sensitive A(+)C wobble pair. The seven-nucleotide hairpin loop contains the high-affinity hnRNP-A1-responsive 5'-UAGU-3' element and a proximal 5'-GAU-3' motif. The NMR structure shows that the heptaloop adopts a well-organized conformation stabilized primarily by base stacking interactions reminiscent of a U-turn. The apex of the loop is quasi-symmetric with UA dinucleotide steps from the 5'-GAU-3' and 5'-UAGU-3' motifs stacking on opposite sides of the hairpin. As a step towards understanding the binding mechanism, we performed calorimetric and NMR titrations of several hnRNP A1 subdomains into ESS3. The data show that the UP1 domain forms a high-affinity (K(d)=37.8±1.1 nM) complex with ESS3 via site-specific interactions with the loop.

Organizational Affiliation