Cryo-EM structures reveal needle-like modes of V2 apex recognition to be a reproducible antibody extended class in rhesus macaques. (a) Top: Cryo-EM reconstruction of 6070-a.01 in complex with Q23.17 MD39 Env at 3.6-Å resolution. The 6070-a.01 heavy and light chains are colored blue and gray, respectively. Envelope gp120, gp41, and N-linked glycans are colored turquoise, pink, and purple, respectively. Middle: Expanded interface view of 6070-a.01 from the top panel to highlight binding position and interactions with apical envelope glycans. Glycans bound by 6070-a.01 are shown in stick representation with transparent surfaces. The N160 glycan reoriented outward and away from the threefold trimer axis is denoted with *. Sulfated tyrosine residues are shown in stick representation to highlight their position within the trimer. Bottom: Further expanded interface view of 6070-a.01 to highlight interactions with apical envelope residues. Interacting residues are depicted in stick representation. Residues at positions corresponding to the conserved five-residue DH3-15*01 gene motif are colored dark red, while the remaining D gene residues are colored pink. Conserved motif position labels are italicized when subjected to SHM. Nitrogen atoms are colored blue, oxygen atoms are colored bright red, and sulfur atoms are colored yellow. Hydrogen bonds and salt bridges (distance < 3.3 Å) are depicted with dashed lines. (b) Top: Cryo-EM reconstruction of T646-a.01 in complex with Q23.17 MD39 Env at 3.5-Å resolution. The T646-a.01 heavy chain is colored orange, and the remainder of the complex is colored similarly to panel a. Middle: Expanded interface view of T646-a.01 from the top panel to highlight binding position and apical glycan interactions is shown similarly to panel a, including the N160 glycan reoriented into a horizontal conformation denoted with *. Bottom: Further expanded interface view of T646-a.01 to highlight apical residue interactions is shown similarly to panel a. (c) Top: Cryo-EM reconstruction of 42056-a.01 in complex with CAP256.wk34.c80 RnS2 SOSIP determined at 4.1-Å resolution. The 42056-a.01 heavy chain is colored light green, and the remainder of the complex is colored similarly to panel a. Middle: Expanded interface view of 42056-a.01 from the top panel to highlight binding position and apical glycan interactions is shown similarly to panel a. Bottom: Further expanded interface view of 42056-a.01 highlight apical residue interactions is shown similarly to panel a. (d) Top: Cryo-EM reconstruction of 44715-a.01 in complex with BG505 DS-SOSIP at 3.9-Å resolution. The 44715-a.01 heavy chain is colored teal, and the remainder of the complex is colored similarly to panel a. Middle: Expanded interface view of 44715-a.01 from the top panel to highlight binding position and apical glycan interactions is shown similarly to panel a. Bottom: Further expanded interface view of 44715-a.01 to highlight apical residue interactions is shown similarly to panel a. (e) Top: Expanded HCDR3 interface view of PGT145 (PDB ID 5V8L) to highlight apical residue interactions is shown similarly to panel a. The tyrosine sulfation posttranslational modification of Y100i was not included in this structure and therefore modeled here. Bottom: Expanded HCDR3 interface side view of the alignment of envelope complex structures of 6070-a.01, T646-a.01, 42056-a.01, and 44715-a.01 determined here to envelope complexes with human Fab’s PCT64-35S (PDB ID 7T74) and PGT145 (PDB ID 5V8L) and rhesus Fab RHA1.V2.01 (PDB ID 6XRT). Alignments were made with gp120 from each complex. Only gp120 of the 6070-a.01 complex is shown for clarity. Sulfated tyrosine residues are shown to highlight their positioning within the trimer.
Figure 3.

Cryo-EM structures reveal needle-like modes of V2 apex recognition to be a reproducible antibody extended class in rhesus macaques. (a) Top: Cryo-EM reconstruction of 6070-a.01 in complex with Q23.17 MD39 Env at 3.6-Å resolution. The 6070-a.01 heavy and light chains are colored blue and gray, respectively. Envelope gp120, gp41, and N-linked glycans are colored turquoise, pink, and purple, respectively. Middle: Expanded interface view of 6070-a.01 from the top panel to highlight binding position and interactions with apical envelope glycans. Glycans bound by 6070-a.01 are shown in stick representation with transparent surfaces. The N160 glycan reoriented outward and away from the threefold trimer axis is denoted with *. Sulfated tyrosine residues are shown in stick representation to highlight their position within the trimer. Bottom: Further expanded interface view of 6070-a.01 to highlight interactions with apical envelope residues. Interacting residues are depicted in stick representation. Residues at positions corresponding to the conserved five-residue DH3-15*01 gene motif are colored dark red, while the remaining D gene residues are colored pink. Conserved motif position labels are italicized when subjected to SHM. Nitrogen atoms are colored blue, oxygen atoms are colored bright red, and sulfur atoms are colored yellow. Hydrogen bonds and salt bridges (distance < 3.3 Å) are depicted with dashed lines. (b) Top: Cryo-EM reconstruction of T646-a.01 in complex with Q23.17 MD39 Env at 3.5-Å resolution. The T646-a.01 heavy chain is colored orange, and the remainder of the complex is colored similarly to panel a. Middle: Expanded interface view of T646-a.01 from the top panel to highlight binding position and apical glycan interactions is shown similarly to panel a, including the N160 glycan reoriented into a horizontal conformation denoted with *. Bottom: Further expanded interface view of T646-a.01 to highlight apical residue interactions is shown similarly to panel a. (c) Top: Cryo-EM reconstruction of 42056-a.01 in complex with CAP256.wk34.c80 RnS2 SOSIP determined at 4.1-Å resolution. The 42056-a.01 heavy chain is colored light green, and the remainder of the complex is colored similarly to panel a. Middle: Expanded interface view of 42056-a.01 from the top panel to highlight binding position and apical glycan interactions is shown similarly to panel a. Bottom: Further expanded interface view of 42056-a.01 highlight apical residue interactions is shown similarly to panel a. (d) Top: Cryo-EM reconstruction of 44715-a.01 in complex with BG505 DS-SOSIP at 3.9-Å resolution. The 44715-a.01 heavy chain is colored teal, and the remainder of the complex is colored similarly to panel a. Middle: Expanded interface view of 44715-a.01 from the top panel to highlight binding position and apical glycan interactions is shown similarly to panel a. Bottom: Further expanded interface view of 44715-a.01 to highlight apical residue interactions is shown similarly to panel a. (e) Top: Expanded HCDR3 interface view of PGT145 (PDB ID 5V8L) to highlight apical residue interactions is shown similarly to panel a. The tyrosine sulfation posttranslational modification of Y100i was not included in this structure and therefore modeled here. Bottom: Expanded HCDR3 interface side view of the alignment of envelope complex structures of 6070-a.01, T646-a.01, 42056-a.01, and 44715-a.01 determined here to envelope complexes with human Fab’s PCT64-35S (PDB ID 7T74) and PGT145 (PDB ID 5V8L) and rhesus Fab RHA1.V2.01 (PDB ID 6XRT). Alignments were made with gp120 from each complex. Only gp120 of the 6070-a.01 complex is shown for clarity. Sulfated tyrosine residues are shown to highlight their positioning within the trimer.

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