The prefusion structure of the HERV-K (HML-2) Env spike complex

Abstract

The human endogenous retrovirus K (HERV-K) is a retrovirus that got assimilated into the human genome in ancient times and has been inherited in our germline ever since. It enters cells using a class-I spike protein (Env) that mediates receptor recognition and membrane fusion. On top of having a biological role during development, HERV-K is activated in amyotrophic lateral sclerosis, various cancers, and other pathological conditions. Antibodies that target the HERV-K spike complex have therapeutic value, flagging the spike as a novel drug target. Here, we use cryo-EM to determine the trimeric structure of the HERV-K spike. The spike presents a distinct structure, which substantially differs from other class-I fusogens. Nevertheless, some general architectural features suggest a common origin with other retroviruses. The ability to structurally characterize the HERV-K spike may facilitate the development of antibody-based therapies.

Keywords: HERV-K; ancient retrovirus; single particle cryo EM; viral spike protein.

Fig. 1.

The overall structure of the HERV-K spike complex. (A) Schematic diagram showing the organization of the HERV-K’s env gene. Areas with solid-colored backgrounds were visible in the EM density map and were modeled. (B) The trimeric structure of the spike complex. The SU (pink) and TM (gray) domains are shown using surface representation from “side” and “top” views on the left and right sides, respectively. N-linked glycans are shown as green spheres. The relative location of the membrane and the dimensions of the spike are annotated. (C) The overall organization of the SU and TM domains. The SU (Left image) and the TM (Right image) domains of a single SU/TM pair are shown as ribbon diagrams, rainbow-colored from the N′ (blue) to the C′ (red), which are annotated. The rest of the spike is shown as a semitransparent surface for reference. (D) The specific organization and local folding regions of the SU domain. A single SU domain is shown as a ribbon diagram, colored and annotated according to the four topological regions. (E) The specific organization of the TM domain with respect to SU. A close-up view of a single TM domain rainbow-colored from the N′ (blue) to the C′ (red). The TM wraps around an SU domain that is illustrated as a semitransparent white surface.

Fig. 2.

The trimeric organization of the HERV-K spike complex. (A) SU–SU interactions are scarce. The SU domains are shown as pink ribbons, and the TM domains are shown using a semitransparent gray surface representation in an illustration of the entire spike from a “side” view. The direct contact points between the SU domains are pointed, and zoom-in views are shown on the Right. The lower zoomed-in image is from a “bottom” view of the spike. (B) Overview of the TM–TM interactions. The three TM domains are shown as ribbons and colored in orange, gray, and livid for TM-1, TM-2, and TM-3, respectively. The three TM domains are shown from a “side” view (Upper image) and from a “top” view (Lower image). The interacting regions in TM-1 are differentially colored and annotated. A red asterisk marks the area inside TM that accommodates SU. (C) A close-up view of the central coiled-coil and the role of h3 and h4 helices in its formation. (D) The various polar interactions between the h2 helix and loop L4/5 on one TM and the h6 and h4 helices on a neighboring TM.

Fig. 3.

TM binds SU in a clamp-like configuration. (A) A single TM/SU pair is shown. The SU is represented as a pink surface, and the TM is shown using a ribbon representation and is colored in gray, green, and blue for the main body, the first and the second “jaws” that grip SU, respectively. (B–D) Detailed description of the TM–SU interactions. The same coloring scheme is used as in “A”. Polar interactions are illustrated with yellow-dashed lines. (E) Detailed view of the TM–SU interactions near the MPER. The image on the right shows a zoom-in view of the indicated region.

Fig. 4.

Putative receptor binding site of the HERV-K spike. (A) Surface electrostatic potential of the spike shown from a “side” view (Upper image) and from a “top” view (Lower image). The electrostatic potential is illustrated by the color (red to blue gradient represents −5 kT/e to 5kT/e). A basic patch on the surface of SU is noted with a green arrow and traced with orange squares. (B) Putative location of heparan sulfate inside the basic patch of SU. A short segment made of glucuronic acid (GlcA) and sulfated glucosamine (GlcNS) was manually fitted into the model and is shown using a gray stick illustration on top of the surface that is colored by the electrostatic potential. (C) Three arginine residues contribute to the basic patch. The residues are shown as sticks underneath a semitransparent surface and are noted. (D) Conserved residues in the SU domain. A single SU domain is shown using a surface representation that is colored according to the relative sequence conservation as calculated by the ConSurf server (43, 44) (Magenta to Dark Cyan represents conserved to variable). The three arginine residues are noted as well as the basic patch that is traced with black squares. (E) The HERV-K spike is shown using surface representation. N-linked glycans are shown as green spheres. The linear epitope of MAb K01 is colored blue. The three arginine residues that make the basic patch are noted in yellow for reference. (F) A close-up view of the linear epitope of MAb K01 on the SU domain. The epitope is colored blue.

Fig. 5.

Acidic-induced triggering of membrane fusion. (A) Syncytia formation assay in cells that express either HERV-K (Left) or an unrelated protein (negative control, Right) following exposure to low-pH buffer. Yellow asterisks mark some of the syncytia. For each condition, two representative images are shown. This assay was repeated twice, each time with multiple technical repeats. (B) The histidine residues in the HERV-K spike. All histidine residues are shown as green spheres. His545 and His578 are indicated. (C) A close-up view of His545. Two TM domains are shown using gray and cyan ribbon representations. Polar contacts are indicated with yellow dashed lines.

Fig. 6.

The HERV-K spike shares structural features with the spike of HIV-1. (A) The HERV-K spike (Left) is shown next to the spike of HIV-1 (Right, PDB:5CJX), using a “side” view. In both spikes, the receptor binding domains (SU and gp120, for HERV-K and HIV-1, respectively) are colored pink, and the fusion domains (TM and gp41, for HERV-K and HIV-1, respectively) are colored gray. The structures are shown using a ribbon diagram and a semitransparent surface representation. (B) The HERV-K and HIV-1 spikes are shown from a “top” view. Orange arrows point to the central coiled coil that is formed by TM/gp41 helices. (C) SU/TM and gp120/gp41 pairs are shown. The four topological regions of HERV-K (as in Fig. 1D) are noted, as well as their equivalent regions in HIV-1.