PDBsum entry 397d

RNA

PDB id: 397d

Contents

DNA/RNA

Metals

_CA ×4

Waters ×178

References listed in PDB file

Key reference

Title

A 1.3-A resolution crystal structure of the HIV-1 trans-Activation response region RNA stem reveals a metal ion-Dependent bulge conformation.

Authors

J.A.Ippolito, T.A.Steitz.

Ref.

Proc Natl Acad Sci U S A, 1998, 95, 9819-9824. [DOI no: 10.1073/pnas.95.17.9819]

PubMed id

9707559

Abstract

The crystal structure of an HIV-1 trans-activation response region (TAR) RNA fragment containing the binding site for the trans-activation protein Tat has been determined to 1.3-A resolution. In this crystal structure, the characteristic UCU bulge of TAR adopts a conformation that is stabilized by three divalent calcium ions and differs from those determined previously by solution NMR. One metal ion, crucial to the loop conformation, binds directly to three phosphates in the loop region. The structure emphasizes the influence of metal ion binding on RNA structure and, given the abundance of divalent metal ion in the cell, raises the question of whether metal ions play a role in the conformation of TAR RNA and the interaction of TAR with Tat and cyclin T in vivo.

Figure 2.
Fig. 2. The refined model superimposed on a 2Fo-Fc electron density map of the TAR RNA Ca1-binding site contoured at 1.3 . Ca1 (yellow sphere) stabilizes the bulge backbone structure through direct ligands with the phosphate oxygens of U23, C24, and G26. Three water molecules, depicted as cyan-colored spheres, complete the octahedral coordination. All Ca^2+-phosphate oxygen distances are 2.3 Å. All Ca^2+-water distances are 2.4 Å.

Figure 3.
Fig. 3. Stereo diagram of the TAR RNA 3-nt bulge region showing the direct and indirect ligands of Ca1, Ca2, and Ca3. Water molecules are colored cyan. Solid yellow bonds denote inner-sphere ligand interactions with the RNA, and black dashed bonds represent outer-sphere coordination. Additional water molecules binding in the bulge region have been omitted for clarity.