7DD4

Solution structure of an RNA derived from the joint region of the TAR and PolyA stems of HIV-1 genomic RNA

PDB DOI: https://doi.org/10.2210/pdb7DD4/pdb
NAKB: 7DD4

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

Deposited: 2020-10-27 Released: 2021-06-09
Deposition Author(s): Obayashi, C.M., Shinohara, Y., Masuda, T., Kawai, G.

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 200
Conformers Submitted: 11
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

Influence of the 5'-terminal sequences on the 5'-UTR structure of HIV-1 genomic RNA.

Obayashi, C.M., Shinohara, Y., Masuda, T., Kawai, G.

(2021) Sci Rep 11: 10920-10920

PubMed: 34035384 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41598-021-90427-9
Primary Citation of Related Structures:
7DD4

PubMed Abstract:
The 5'-UTR of HIV-1 genomic RNA is known to form specific structures and has important functions. There are three 5'-terminal sequences, G1, G2 and G3, with different localizations in the cell and virion particles as well as different efficiencies in translation and reverse transcription reactions. In the present study, the structural characteristics of the joint region between the TAR and PolyA stems was analysed, and it was found that small differences in the 5'-terminus affect the conformational characteristics of the stem-loop structures. In the G1 form, the two stems form a coaxial stem, whereas in the G2 and G3 forms, the two stems are structurally independent of each other. In the case of the G1 form, the 3'-flanking nucleotides of the PolyA stem are included in the stable coaxial stem structure, which may affect the rest of the 5'-UTR structure. This result demonstrates that the local conformation of this functionally key region has an important role in the function of the 5'-UTR.

Organizational Affiliation

Department of Life Science, Graduate School of Advanced Engineering, Chiba Institute of Technology, Tsudanuma, 2-17-1, Narashino-shi, Chiba, 275-0016, Japan.