Cryo-electron tomographic structure of an immunodeficiency virus envelope complex in situ

Abstract

The envelope glycoprotein (Env) complexes of the human and simian immunodeficiency viruses (HIV and SIV, respectively) mediate viral entry and are a target for neutralizing antibodies. The receptor binding surfaces of Env are in large part sterically occluded or conformationally masked prior to receptor binding. Knowledge of the unliganded, trimeric Env structure is key for an understanding of viral entry and immune escape, and for the design of vaccines to elicit neutralizing antibodies. We have used cryo-electron tomography and averaging to obtain the structure of the SIV Env complex prior to fusion. Our result reveals novel details of Env organisation, including tight interaction between monomers in the gp41 trimer, associated with a three-lobed, membrane-distal gp120 trimer. A cavity exists at the gp41-gp120 trimer interface. Our model for the spike structure agrees with previously predicted interactions between gp41 monomers, and furthers our understanding of gp120 interactions within an intact spike.

Figure 1. Three-Dimensional Reconstruction of SIV Virions from Cryo-Electron Tomography

(A) A slice through the xy plane of a reconstructed tomogram from the −6-μm defocus dataset. The spike complexes are clearly visible on the viral surface. Some of the cores appear disrupted, reflecting AT-2 treatment. Scale bar represents 100 nm. (B) Surface rendering of one of the virions. The membrane is represented in blue, the core in red and the spikes in orange. (C) The same virus as in (B) viewed after removing half of the viral envelope along the dotted line to reveal the core. The density between the core and the membrane has not been rendered.

Figure 2. Reconstruction of the Env Spike, Filtered to 28 Å, and Rendered

(A) A rendered view of the complex at a 2 sigma contour level. The chirality of the distal portion is evident. (B) As in (A), rotated 60° around the 3-fold symmetry axis. (C) A slab through the density in the orientation represented in panel (B), revealing the cavity at the centre of the structure. The membrane is coloured in cyan. The volume corresponding to gp41 has been coloured in gray, and the remaining gp120 volume in orange. Scale bar = 100 Å.

Figure 3. Fitting of the Molecular Model of Unliganded SIV gp120 into the Reconstruction

(A) and (B) Views of the first fitting (shown from above in panel [A] and from the side in panel [B]). The variable loops V1V2 (black), V4, and V5 (light blue) are positioned on the surface of the trimer, whereas V3 (red) is closer to the trimer interface. The receptor binding pocket (magenta) is exposed, although partially protected by sugars (blue) and variable loops. The bridging sheet (green) is hidden at the trimer–gp41 interface. Sugar residues are exposed on the surface. (C) and (D) Views of the second fitting (shown from above in panel [C] and from the side in panel [D]). The colour code is the same as in panels (A) and (B). Variable loops V1V2, V3, V4, and V5 are exposed on the surface of the trimer. The receptor binding pocket is also exposed and partially protected by sugars. The bridging sheet is exposed, and the V3 loop could protect it from antibody binding. Sugar residues are exposed.

Figure 4. Model for HIV/SIV Receptor Engagement, Based on the First Proposed Fitting

(A) The Env complex before CD4 binding. The bridging sheet is not accessible to co-receptor and antibodies, and the V3 loop is at the trimer interface. (B) CD4 binding causes a conformational change and an overall rotation of the gp120 molecule. The V3 loop binds selectively to co-receptor, and the bridging sheet becomes exposed and available for co-receptor binding.