Structural basis for viral late-domain binding to Alix

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Abstract

The modular protein Alix is a central node in endosomal-lysosomal trafficking and the budding of human immunodeficiency virus (HIV)-1. The Gag p6 protein of HIV-1 contains a LYPxnLxxL motif that is required for Alix-mediated budding and binds a region of Alix spanning residues 360–702. The structure of this fragment of Alix has the shape of the letter 'V' and is termed the V domain. The V domain has a topologically complex arrangement of 11 α-helices, with connecting loops that cross three times between the two arms of the V. The conserved residue Phe676 is at the center of a large hydrophobic pocket and is crucial for binding to a peptide model of HIV-1 p6. Overexpression of the V domain inhibits HIV-1 release from cells. This inhibition of release is reversed by mutations that block binding of the Alix V domain to p6.

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Figure 1: Structure and LYPxnLxxL motif–binding site of the Alix V domain.
Figure 2: Secondary structures and sequence alignment of human Alix and Alix orthologs (from Drosophila melanogaster, Caenorhabditis elegans, Dictyostelium discoideum, Arabidopsis thaliana and Saccharomyces cerevisiae).
Figure 3: In vitro binding of an HIV-1 p6 LYPxnLxxL-based 16-residue peptide to Alix.
Figure 4: A functional hydrophobic pocket is required for inhibition of HIV-1 release.
Figure 5: Virus budding defects visualized by electron microscopy.

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Acknowledgements

We thank J. Kim, G. Miller and U. Munshi for many contributions to the early stages of this project, F. Soheilian for EM support, D.E. Anderson for mass spectrometry support, B. Beach and T. Leonard for advice and discussions and J. Bonifacino for the use of his calorimeter. C. Hill and W. Sundquist independently determined this structure and suggested the term 'V domain', which we have adopted. Use of the National Synchrotron Light Source at Brookhaven National Laboratory was supported by the US Department of Energy, Basic Energy Sciences, Office of Science, under contract no. DE-AC02-98CH10886. HIV-Ig was obtained through the AIDS Research and Reference Reagent Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, NIH. This research was supported by the Intramural Research Program of the NIH, National Institute of Diabetes and Digestive and Kidney Diseases (J.H.H.) and National Cancer Institute, Center for Cancer Research (E.O.F.). Funds were also obtained from the Intramural AIDS Targeted Antiviral Program (J.H.H. and E.O.F.) and from the National Cancer Institute under contract N01-CO-12400 (K.N.).

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Correspondence to James H Hurley.

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Lee, S., Joshi, A., Nagashima, K. et al. Structural basis for viral late-domain binding to Alix. Nat Struct Mol Biol 14, 194–199 (2007) doi:10.1038/nsmb1203

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