Subunit organization of the membrane-bound HIV-1 envelope glycoprotein trimer

Journal name:
Nature Structural & Molecular Biology
Volume:
19,
Pages:
893–899
Year published:
DOI:
doi:10.1038/nsmb.2351
Received
Accepted
Published online

Abstract

The trimeric human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) spike is a molecular machine that mediates virus entry into host cells and is the sole target for virus-neutralizing antibodies. The mature Env spike results from cleavage of a trimeric glycoprotein precursor, gp160, into three gp120 and three gp41 subunits. Here, we describe an ~11-Å cryo-EM structure of the trimeric HIV-1 Env precursor in its unliganded state. The three gp120 and three gp41 subunits form a cage-like structure with an interior void surrounding the trimer axis. Interprotomer contacts are limited to the gp41 transmembrane region, the torus-like gp41 ectodomain and a trimer-association domain of gp120 composed of the V1, V2 and V3 variable regions. The cage-like architecture, which is unique among characterized viral envelope proteins, restricts antibody access, reflecting requirements imposed by HIV-1 persistence in the host.

At a glance

Figures

  1. The cryo-EM structure of the membrane-bound HIV-1 Env trimer at ~11-Å resolution.
    Figure 1: The cryo-EM structure of the membrane-bound HIV-1 Env trimer at ~11-Å resolution.

    (a) The reconstruction of the HIV-1JR-FL Env(−)ΔCT trimer is shown as a solid surface viewed from a perspective parallel to the viral membrane. The approximate boundaries of the transmembrane region and ectodomain are indicated. (b) The Env trimer reconstruction is visualized at two different levels of contour, illustrated as a meshwork (lower level) and a solid-surface representation (higher level). (c) The Env trimer reconstruction in a solid-surface representation is viewed from the perspective of the target cell, at the same contour level as that shown in a. (d) The Env trimer reconstruction is shown at two different levels of contour in the same way as in b, viewed from the perspective of the target cell. (e) The images show typical reference-free class averages produced by maximum-likelihood alignment with no C3 symmetry imposed. Scale bar, 10 nm. See Supplementary Figures 3 and 4, Supplementary Movies 2 and 3 for more details.

  2. The map segmentation of an Env protomer.
    Figure 2: The map segmentation of an Env protomer.

    (a,b) The map segmentation of an Env protomer in solid-surface representation is wrapped in a meshwork representation of the Env trimer, viewed from a perspective parallel to the viral membrane. Two different Env protomers are segmented in a and b. The segments approximately correspond to the indicated gp120 and gp41 domains. The red dashed circle indicates the approximate position of the CD4-binding site on the gp120 subunit. (c) The segmentation is viewed from the perspective of the target cell.

  3. Fit of the crystal structure of CD4-bound gp120 core into the cryo-EM density of the unliganded Env trimer in two different configurations.
    Figure 3: Fit of the crystal structure of CD4-bound gp120 core into the cryo-EM density of the unliganded Env trimer in two different configurations.

    (a,b) The CD4-bound gp120 core structure (PDB 3JWD)8 was fitted into the local Env-trimer cryo-EM density identified by segmentation as the gp120 inner domain and outer domain (see Fig. 2). This fitting configuration represents the best fit of the gp120 core crystal structure, taking into account both the inner and outer domains. The cryo-EM density is shown as a meshwork representation. The red arrow in a marks the interdomain cavity in the gp120 subunit. The gp120 core is missing the V1, V2 and V3 variable regions8. The inner domain and outer domain of the gp120 core crystal structure are colored orange and dark blue, respectively. A fraction of the residues of the gp120 outer domain do not fit in the cryo-EM density in this fitting configuration, suggesting conformational differences between the unliganded and CD4-bound states. (c,d) The gp120 outer domain from the CD4-bound gp120 core structure8 was fitted into the cryo-EM density of the Env trimer, without consideration of the fit of the gp120 inner domain. This allows a much better fitting of the gp120 outer domain than that seen in a and b; only the LV5 variable loop has a few residues out of the cryo-EM density. Under the same fitting configuration, the inner domain of the CD4-bound gp120 core is largely outside the Env trimer cryo-EM density (not shown). This observation suggests that the gp120 inner domain rotates with respect to the outer domain upon binding CD4.

  4. The gp120 trimer-association domains.
    Figure 4: The gp120 trimer-association domains.

    (a) The segmented local densities of gp120 that associate near the trimer axis are shown as solid surfaces wrapped in a meshwork representing the overall Env trimer, viewed from the perspective of the target cell. Note the central triangular junction (yellow) with a diameter of around 1.5 nm. (b) The gp120 trimer-association domain segments are viewed from the perspective of the viral membrane. Three arms extend from the V3 base of each gp120 subunit toward the trimer axis and appear to support the central triangular junction. The approximate positions of the V1/V2 stem and V3 base are labeled in a and b. (c) The gp120 trimer-association domain segments are viewed from a perspective parallel to the viral membrane.

  5. Architecture of gp41 trimer association.
    Figure 5: Architecture of gp41 trimer association.

    (a,b) The gp41 segments are shown as solid surfaces wrapped in a meshwork representing the overall Env trimer, viewed from a perspective parallel to the viral membrane (a) and from the perspective of the viral membrane (b). (c,d) The gp41 ectodomain segments that form the torus and contribute to interprotomer interactions are shown. The views are from a perspective parallel to the viral membrane (c) and from the perspective of the viral membrane (d).

  6. Comparison of the 11-Å cryo-EM structure of the trimeric HIV-1 Env precursor with the 20-Å electron tomographic model of the native HIV-1 Env trimer on virions.
    Figure 6: Comparison of the 11-Å cryo-EM structure of the trimeric HIV-1 Env precursor with the 20-Å electron tomographic model of the native HIV-1 Env trimer on virions.

    (a) The 20-Å model of the HIV-1 Env trimer on virions (EMDB ID: EMD-5019) (gray surface)14 and the 11-Å model of the HIV-1 Env precursor (cyan surface) are superimposed, with the trimer axis used as a common reference. Both models are shown at a comparable level of contour. (b) The same models and levels of contour as in a are shown, but the 20-Å tomographic model of the virion Env trimer is shown as a transparent gray surface. (c) The 11-Å cryo-EM model (left) and the 20-Å tomographic model (right) are visualized side by side as solid-surface representations at higher levels of contour than those shown in a and b. Upper and lower inserts show the superposition of the two models, with the 11-Å cryo-EM model shown as a meshwork representation and the 20-Å tomographic model as a transparent surface representation.

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Referenced accessions

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Affiliations

  1. Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA.

    • Youdong Mao,
    • Liping Wang,
    • Christopher Gu,
    • Alon Herschhorn,
    • Shi-Hua Xiang,
    • Hillel Haim &
    • Joseph Sodroski
  2. Department of Medicine, Division of Viral Pathogenesis, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.

    • Xinzhen Yang
  3. Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Boston, Massachusetts, USA.

    • Joseph Sodroski
  4. Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA.

    • Joseph Sodroski
  5. Present address: Nebraska Center for Virology, School of Veterinary Medicine and Biomedical Sciences, University of Nebraska–Lincoln, Lincoln, Nebraska, USA.

    • Shi-Hua Xiang

Contributions

Y.M. and J.S. conceived this study. Y.M. designed experimental protocols; Y.M., L.W., C.G., A.H., S.-H.X., H.H., X.Y. and J.S. performed the research; Y.M. and J.S. analyzed the results and wrote the paper.

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The authors declare no competing financial interests.

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