Research ArticleIMMUNOLOGY

Structural basis of broad HIV neutralization by a vaccine-induced cow antibody

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Science Advances  27 May 2020:
Vol. 6, no. 22, eaba0468
DOI: 10.1126/sciadv.aba0468
  • Fig. 1 NC-Cow1 crystal structures.

    (A) Crystal structure of unliganded Fab NC-Cow1 at 2.1 Å resolution with heavy chain in light blue and light chain in pink. VL, variable region of immunoglobulin light chain. VH, variable region of immunoglobulin heavy chain. (B) The knob at the tip of the 60-residue CDR H3 contains three β strands (yellow, green, and blue), connected by two loops, with three disulfide bonds (cyan, red, and magenta). (C) BG505 SOSIP.664 Env trimer (gray) in complex with three NC-Cow1 Fabs (light chain, pink; heavy chain, blue), three PGT128 Fabs (green), and three 35022 Fabs (yellow). (D) The crystallographic asymmetric unit contains one SOSIP protomer (gp120 and gp41) and one each of the NC-Cow1, PGT128, and 35022 Fabs. The PGT128 and 35022 Fabs were added to help obtain diffraction-quality crystals (19, 20).

  • Fig. 2 Knob interactions of NC-Cow1 with gp120 in SOSIP Env trimer.

    (A) The x-ray (light blue, heavy chain; light pink, light chain; white, gp120) and cryo-EM (light yellow, heavy chain; dark gray, gp120) structures are superimposed by their gp120 components in the BG505 SOSIP.664 Env trimer and show nearly identical binding of the NC-Cow1 CDR H3 knob. (B) The gp120 CD4BL (residues 362 to 374), V5 region (458 to 469), and D loop (275 to 283) in the crystal structure are colored pink, light yellow, and light green, respectively. The glycan (green, carbons; red, oxygens) at Asn197 contacts the CDR H3 knob, while some of the sugar moieties in the glycans at Asn276 and Asn234 have ordered electron density but make little or no contact with the Fab. (C) Knob residues contacting gp120 are highlighted with color coding as in (B).

  • Fig. 3 Comparison of binding of NC-Cow1 and CD4 to gp120.

    The gp120 is shown with a white surface, with the Asp368 oxygen atoms colored red and the Asp side chain in stick representation. NC-Cow1 (A) mimics the interaction of CD4 (B) through insertion of an aromatic residue into the Phe43 binding pocket (TyrD31) and through formation of a salt bridge from ArgD11 to gp120 Asp368.

  • Fig. 4 NC-Cow1 Fab alanine mutants affect binding and neutralization.

    (A) Sequence alignment of NC-Cow1 CDR H3 with the germline–encoded IGHV1-7, IGHD8-2, and IGHJ2-4 segments. The numbering scheme for the bovine ultralong CDR H3 region follows reference (12). V, D, and J gene usage was determined as described in (11) using the IMGT database and BLASTn. Twenty-five residues in the knob and stalk region (underlined) were mutated to alanine. Cysteines are shaded in yellow, and the disulfide pattern is indicated above the sequence. (B) Residues that are important for Fab binding and neutralization to BG505 SOSIP.664 trimers. Ratios of half-maximal effective binding concentrations (EC50) of each mutant relative to wild-type Fab (set to 1) were calculated. The neutralization potency of each alanine mutant was measured using IC50. The EC50 and IC50 values are shaded yellow, orange, and red according to the color scheme. For the ELISA measurements: NB, no binding activity/curve could be generated; for the neutralization measurements: NN, no neutralization detected. The surface areas buried on gp120 by each Fab residue (as calculated from the crystal structure) are shown on the right.

  • Fig. 5 NC-Cow1 binds the CD4 binding site with a compact footprint.

    (A) Highlighted on the BG505 SOSIP.664 trimer (top left) are residues from the CD4BL (362 to 374, pink), V5 loop (458 to 469, pale yellow), and D loop (275 to 283, pale green). The buried molecular surfaces on the trimer or gp120 core are highlighted in red for CD4 (PDB 6CM3), NC-Cow1, human bnAb N6 (PDB 5TE7) (top row), and NIH45-46 (PDB 5D9Q) (bottom left) overlaid onto the key CD4bs elements. With the exception of N6, comparisons were made only to structures determined for Fabs in complex with the BG505 SOSIP trimer. While many structures exist for CD4 binding site Fabs bound to deglycosylated gp120 cores, these may appear to have smaller epitopes because of lack of contact with glycans, missing variable regions, and neighboring trimer subunits. Wild-type N6 has not been determined in complex with this trimer but has been included in the comparison (bound to gp120 core), as it is the most potent and broadly neutralizing CD4 binding site Fab determined to date. The V3 base/N332 glycan and apex binding sites for PGT128 (PDB 5ACO) and PGT145 (PDB 5V8L) (bottom middle and bottom right), respectively, are also shown for comparison. The unbound, CD4-bound, NC-Cow1–bound, and NIH45-46–bound trimers and the N6-bound gp120 core are all in the same orientation, with their gp120 subunits superimposed. The PGT128 trimer is shown rotated ~25° about the vertical trimer axis, and the PGT145-bound trimer is shown rotated ~90° about a horizontal axis. (B) The binding footprint for CD4 (left; 6CM3), NC-Cow1 (middle), and NIH45-46 (right; 5D9Q) on the BG505 SOSIP.664 trimer is outlined in white. The SOSIP surface is colored in a rainbow spectrum by the Wu-Kabat variability (24) of each residue (see table S3 for numerical values), with conserved regions colored dark blue and highly variable regions colored red. The darkest blue corresponds to Wu-Kabat variability values of 3 or less, while the red corresponds to Wu-Kabat variability value over 80, as shown on the color bar.

  • Fig. 6 Comparison of NC-Cow1 with human bnAb PGT145.

    (A) NC-Cow1 with light chain in light gray, heavy chain in dark gray, and CDR H3 in red. (B) PGT145, colored as in (A), from PDB 3U1S.

Supplementary Materials

  • Supplementary Materials

    Structural basis of broad HIV neutralization by a vaccine-induced cow antibody

    Robyn L. Stanfield, Zachary T. Berndsen, Ruiqi Huang, Devin Sok, Gabrielle Warner, Jonathan L. Torres, Dennis R. Burton, Andrew B. Ward, Ian A. Wilson, Vaughn V. Smider

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    • Figs. S1 to S7
    • Tables S1 to S4
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