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Complexes of HIV-1 RT, NNRTI and RNA/DNA hybrid reveal a structure compatible with RNA degradation

Abstract

Hundreds of structures of type 1 human immunodeficiency virus (HIV-1) reverse transcriptase (RT) have been determined, but only one contains an RNA/DNA hybrid. Here we report three structures of HIV-1 RT complexed with a non-nucleotide RT inhibitor (NNRTI) and an RNA/DNA hybrid. In the presence of an NNRTI, the RNA/DNA structure differs from all prior nucleic acid–RT structures including the RNA/DNA hybrid. The enzyme structure also differs from all previous RT–DNA complexes. Thus, the hybrid has ready access to the RNase-H active site. These observations indicate that an RT–nucleic acid complex may adopt two structural states, one competent for DNA polymerization and the other for RNA degradation. RT mutations that confer drug resistance but are distant from the inhibitor-binding sites often map to the unique RT-hybrid interface that undergoes conformational changes between two catalytic states.

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Figure 1: HIV-1 RT complexed with an RNA/DNA hybrid and an NNRTI.
Figure 2: Structure comparison of HIV-1 RT.
Figure 3: Structural comparison of WT22efv and RT–DNA–nvp (3V81)29.
Figure 4: Structural comparison of nucleic acid complexed with RT.
Figure 5: The RNA/DNA hybrid structure is compatible with RNase H cleavage.
Figure 6: The altered p51-p66 subunit interface interacts with the RNA/DNA hybrid.

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Acknowledgements

We thank D. Leahy and M. Nowotny for editing and critiquing the manuscript, C. Biertümpfel and Y. Zhao for help with data collection and J.H.D. Cate (University of California, Berkeley, Berkeley, California, USA) for the ModeVector script to make Figures 2 and 3a. The research was supported by the US National Institutes of Health Intramural AIDS Targeted Anti-viral Program (IATAP) and the intramural research programs of the US National Institute of Diabetes and Digestive and Kidney Diseases (W.Y., M.L. and L.T.) and the US National Cancer Institute (S.F.J.L.G. and J.T.M.).

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Contributions

J.T.M. prepared the HIV-1 RT mutants and proteins. L.T. made the RT–RNA/DNA–NNRTI complexes, grew the crystals and collected the diffraction data. M.L. refined the structures, and W.Y. carried out structure comparisons. W.Y. and S.F.J.L.G. originated the project. M.L., L.T., S.F.J.L.G. and W.Y. prepared the manuscript. All authors discussed the results and commented on the manuscript.

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Correspondence to Wei Yang.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6 (PDF 2802 kb)

Supplementary Video 1

Video 1 Structural differences between RT-NNRTI and the RT-RNA/DNA-NNRTI complex (Video1.mov) (MOV 2259 kb)

Supplementary Video 2

Video 2 Structural differences between RT-DNA-dATP and the RT-RNA/DNA-NNRTI complex. (Video2.mov) (MOV 2231 kb)

Supplementary Video 3

Video 3 Morphing of nucleic acid complexed with HIV-1 RT from the DNA polymerization to RNA degradation-compatible state. (video3.mov) (MOV 1962 kb)

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Lapkouski, M., Tian, L., Miller, J. et al. Complexes of HIV-1 RT, NNRTI and RNA/DNA hybrid reveal a structure compatible with RNA degradation. Nat Struct Mol Biol 20, 230–236 (2013). https://doi.org/10.1038/nsmb.2485

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