PDBsum entry 1duq

RNA

PDB id: 1duq

Contents

DNA/RNA

Metals

_NA ×10

Waters ×83

References listed in PDB file

Key reference

Title

The crystal structure of the rev binding element of HIV-1 reveals novel base pairing and conformational variability.

Authors

L.W.Hung, E.L.Holbrook, S.R.Holbrook.

Ref.

Proc Natl Acad Sci U S A, 2000, 97, 5107-5112. [DOI no: 10.1073/pnas.090588197]

PubMed id

10792052

Abstract

The crystal and molecular structure of an RNA duplex corresponding to the high affinity Rev protein binding element (RBE) has been determined at 2.1-A resolution. Four unique duplexes are present in the crystal, comprising two structural variants. In each duplex, the RNA double helix consists of an annealed 12-mer and 14-mer that form an asymmetric internal loop consisting of G-G and G-A noncanonical base pairs and a flipped-out uridine. The 12-mer strand has an A-form conformation, whereas the 14-mer strand is distorted to accommodate the bulges and noncanonical base pairing. In contrast to the NMR model of the unbound RBE, an asymmetric G-G pair with N2-N7 and N1-O6 hydrogen bonding, is formed in each helix. The G-A base pairing agrees with the NMR structure in one structural variant, but forms a novel water-mediated pair in the other. A backbone flip and reorientation of the G-G base pair is required to assume the RBE conformation present in the NMR model of the complex between the RBE and the Rev peptide.

Figure 2.
Fig. 2. Stereo view of the least-squares superposition of type I (black) and type II (red) helices viewed perpendicular to the helix axis and into the major groove of the internal loop. The bulged nucleotides A21 and U25 protrude from the helix. The helical axes are bent by 17° for type I and 8° for type II duplexes.

Figure 6.
Fig. 6. Stacking interactions between base pairs in and around the duplex 1 RBE internal loop viewed perpendicular to the base pair plane. (a) G104-C127 and G105-A126. (b) G105-A126 and G106-G124. (c) G106-G124 and C107-G123.