HIV-1 envelope glycoprotein structure

Abstract

The trimeric envelope glycoprotein of HIV-1, composed of gp120 and gp41 subunits, remains a major target for vaccine development. The structures of the core regions of monomeric gp120 and gp41 have been determined previously by X-ray crystallography. New insights into the structure of trimeric HIV-1 envelope glycoproteins are now coming from cryo-electron tomographic studies of the gp120/gp41 trimer as displayed on intact viruses and from cryo-electron microscopic studies of purified, soluble versions of the ectodomain of the trimer. Here, we review recent developments in these fields as they relate to our understanding of the structure and function of HIV-1 envelope glycoproteins.

Figure 1. gp120 structures obtained by X-ray crystallography

To provide a comparison of the similarities and differences between the various gp120 structures determined by X-ray crystallography, three different sets of superpositions are presented. (A) Superposition of all 24 reported structures of gp120 variants. The PDB IDs of entries included in the superposition are 3NGB, 3TGT, 3SE9, 3SE8, 4DKR, 4DKQ, 4DKP, 4DKO, 3U7Y, 3RJQ, 3TGS, 3TGR, 3TIH, 3TGQ, 3JWD, 2B4C, 2QAD, 3HI1, 1GC1, 2I5Y, 1YYL, 3LQA, 3IDX, and 2NY7. The 3TYG structure was excluded because it does not contain the inner domain of gp120, although the rest of the polypeptide assumes the same conformation as the structures shown here [22]. (B) Color-coded representation of the superposition shown in (A) to display the extent of variation observed in different regions of gp120. 3NGB coordinates are used as the reference structure. The root-mean-square-deviation of the Cα backbone of gp120 between all 24 sets of coordinates is < 1 Å for blue regions, 2 Å for white regions, and 4 Å for red regions. N- and C-termini of the 3NGB gp120 core are marked. The dashed line illustrates the overall organization of gp120 into an inner domain that faces the interior and an outer domain that faces the exterior. (C, D) Superpositions of the 14 most recent sets of gp120 coordinates, reported between 2010 and 2012, are displayed as in panels (A) and (B). (E, F) As in panels (A) and (B), superpositions of the four variants of gp120 structure reported to be present within the same three-dimensional crystal of the gp120 core bound to Fab fragments of the VRC01 antibody are included. The core regions of the gp120 structures are remarkably similar to each other, while the stumps of the variable loop regions included in the crystallized polypeptides are most prone to variation (red).

Figure 2. Changes in molecular architecture of trimeric gp120 complexed to different CD4-binding site and co-receptor binding site ligands

(A–F)Top views of density maps of native trimeric Env in unliganded (A), VRC01-bound (B), b12-bound (C), A12-bound (D), soluble CD4-bound (E) and 17b-bound (F) states. In each case, density maps at resolutions of ~ 20 Å are shown fitted with three copies either of gp120 coordinates or of gp120 bound to the respective ligands: PDB IDs are 3DNN, 3NGB, 2NY7, 3RJQ, 1GC1 and 1GC1, respectively. Chains are colored red for gp120 core, blue for VRC01, cyan for b12, light sea green for A12, yellow for soluble CD4, and forest green for 17b. (G) Schematic representation of trimeric Env in various states, presented with the same coloring arrangement and in the same order in which they appear in panels (A–F). Trimeric gp120 is in the “closed” state in unliganded and VRC01-bound states, “partially open” in b12- and A12-bound states and “fully open” in soluble CD4- and 17b-bound states.

Figure 3. Comparison of effects of VRC01 and sCD4 binding on gp120 monomers vs. native Env trimers

(A, B) Views from two different directions of the superposed structures of the gp120-sCD4-17b complex (PDB ID: 1GC1) and the gp120-VRC01 complex (PDB ID: 3NGB). For clarity, only those regions of VRC01 (blue) and sCD4 (yellow) that are in close proximity to gp120 (light grey for the VRC01 bound conformation, and dark grey for sCD4 bound conformation) are shown. The orientation of the stumps of the V1V2 (red) and V3 (green) loops on the gp120 surface provides a visual marker for gp120 conformation. (C, D) Top views of the surface representations of trimeric gp120 derived by fitting three copies of the gp120-VRC01 structure (C) or gp120-sCD4 structure (D) into density maps determined by cryo-electron tomography from the respective complexes of native trimeric Env. The quaternary conformation of trimeric gp120 in the VRC01 complex is closed, and similar to unliganded trimeric Env, while the quaternary conformation of the sCD4 complex is open, with large rearrangements of gp120 as indicated by changes in position of the V1V2 and V3 loop regions. The color scheme is the same as is used in panels (A) and (B).

Figure 4. Structures of gp41 trimers visualized by X-ray crystallography and of gp41 helices within soluble gp140 trimers visualized by cryo-electron microscopy

(A, B) Superposition of 24 structures reported for trimeric variants of gp41 N-terminal and C-terminal helices in the canonical post-fusion “six-helix bundle” conformation, shown as top (A) and front (B) views. All gp41 coordinates were aligned to the 1AIK structure [44]. The PDB IDs of entries included in the superposition are 1AIK, 2X7R, 2XRA, 3MAC, 3MA9, 2CMR, 3VIE, 1F23, 3AHA, 2Z2T, 3P30, 1ENV, 1K34, 1DLB, 1SZT, 1DF4, 3CP1, 3CYO, 2OT5, 1QR9, 1I5X, 1I5Y, 3VTP, and 3K9A. (C, D) Top and front views of the structure, determined by cryo-electron microscopy, at ~ 9 Å resolution, of trimeric gp140 in an activated, but pre-fusion conformation [36]. The structure represents a complex between the entire ectodomain of trimeric Env and Fab fragments of the monoclonal antibody 17b. The three central densities are assigned to the three copies of the N-heptad repeat helix in gp41, which form a three-helix motif that is more open than that observed in the post-fusion structures shown in panels (A) and (B). The density map is shown fitted with coordinates for the gp120 core (red), heavy (green) and light (yellow) chains of the Fv fragment of the 17b antibody, and the gp41 N-terminal helices (cyan). The gp120 and 17b coordinates are from PDB structure 1GC1 [9], while the gp41 coordinates are from PDB structure 1AIK [44].