Cryo-EM structures reveal combined modes of V2 apex recognition to be a reproducible antibody extended class in rhesus macaques. (a) Top: Cryo-EM reconstruction of V031-a.01 in complex with BG505 DS-SOSIP at 3.1-Å resolution. The V031-a.01 heavy and light chains are colored blue and gray, respectively. Env gp120, gp41, and N-linked glycans are colored turquoise, pink, and purple, respectively. Bottom: Expanded interface view of V031-a.01 from the top panel to highlight binding position and interactions with apical envelope glycans. Glycans bound by V031-a.01 are shown in stick representation with transparent surfaces. Sulfated tyrosine residues are shown in stick representation to highlight their position within the trimer. (b) Further expanded interface views of V031-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. Top: interactions made with the primary recognized C strand. The orientations of the C-strand and HCDR3 β-strand mainchain interactions are labeled in the top left corner. Bottom: Interactions mediated by HCDR3 residues inserted into the trimer hole. (c) Top: Cryo-EM reconstruction of 6561-a.01 in complex with Ce1176 RnS2 SOSIP at 4.1-Å resolution. The 6561-a.01 heavy chain is colored orange, and the remainder of the complex is depicted similarly to panel a. Bottom: Expanded interface view of 6561-a.01 from the top panel to highlight binding position and interactions with apical glycans is shown similarly to panel a. (d) Further expanded interface views of 6561-a.01 to highlight interactions with apical residues are shown similarly to panel b. (e) Top: Cryo-EM reconstruction of 40591-a.01 in complex with T250.4 RnS2 SOSIP at 4.2-Å resolution. The 40591-a.01 heavy chain is colored orange, and the remainder of the complex is colored similarly to panel a. Bottom: Expanded interface view of 40591-a.01 from the top panel to highlight binding position and interactions with apical Env glycans is shown similarly to panel a. (f) Further expanded interface views of 40591-a.01 to highlight interactions with apical Env residues are shown similarly to panel b. (g) Expanded HCDR3 interface views of VRC26.25 (PDB ID 6VTT) to highlight apical envelope residue interactions are shown similarly to panel b. Left: Interactions are mediated by HCDR3 residues inserted into the trimer hole. Right: Interactions mediated by all other Fab residues. (h) Expanded HCDR3 interface side view of the alignment of envelope complex structures of V031-a.01, 6561-a.01, and 40591-a.01 determined here to the envelope complex of VRC26.25 (PDB ID 6VTT). Alignments were made with gp120 from each complexes, while only gp120 of the VRC26.25 complex is shown for clarity. Sulfated tyrosine residues are shown to highlight their positioning within the trimer. Residue F100e of 40591-a.01 is also shown since it is similarly inserted into the trimer hole but cannot be modified posttranslationally.
Figure 5.

Cryo-EM structures reveal combined modes of V2 apex recognition to be a reproducible antibody extended class in rhesus macaques. (a) Top: Cryo-EM reconstruction of V031-a.01 in complex with BG505 DS-SOSIP at 3.1-Å resolution. The V031-a.01 heavy and light chains are colored blue and gray, respectively. Env gp120, gp41, and N-linked glycans are colored turquoise, pink, and purple, respectively. Bottom: Expanded interface view of V031-a.01 from the top panel to highlight binding position and interactions with apical envelope glycans. Glycans bound by V031-a.01 are shown in stick representation with transparent surfaces. Sulfated tyrosine residues are shown in stick representation to highlight their position within the trimer. (b) Further expanded interface views of V031-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. Top: interactions made with the primary recognized C strand. The orientations of the C-strand and HCDR3 β-strand mainchain interactions are labeled in the top left corner. Bottom: Interactions mediated by HCDR3 residues inserted into the trimer hole. (c) Top: Cryo-EM reconstruction of 6561-a.01 in complex with Ce1176 RnS2 SOSIP at 4.1-Å resolution. The 6561-a.01 heavy chain is colored orange, and the remainder of the complex is depicted similarly to panel a. Bottom: Expanded interface view of 6561-a.01 from the top panel to highlight binding position and interactions with apical glycans is shown similarly to panel a. (d) Further expanded interface views of 6561-a.01 to highlight interactions with apical residues are shown similarly to panel b. (e) Top: Cryo-EM reconstruction of 40591-a.01 in complex with T250.4 RnS2 SOSIP at 4.2-Å resolution. The 40591-a.01 heavy chain is colored orange, and the remainder of the complex is colored similarly to panel a. Bottom: Expanded interface view of 40591-a.01 from the top panel to highlight binding position and interactions with apical Env glycans is shown similarly to panel a. (f) Further expanded interface views of 40591-a.01 to highlight interactions with apical Env residues are shown similarly to panel b. (g) Expanded HCDR3 interface views of VRC26.25 (PDB ID 6VTT) to highlight apical envelope residue interactions are shown similarly to panel b. Left: Interactions are mediated by HCDR3 residues inserted into the trimer hole. Right: Interactions mediated by all other Fab residues. (h) Expanded HCDR3 interface side view of the alignment of envelope complex structures of V031-a.01, 6561-a.01, and 40591-a.01 determined here to the envelope complex of VRC26.25 (PDB ID 6VTT). Alignments were made with gp120 from each complexes, while only gp120 of the VRC26.25 complex is shown for clarity. Sulfated tyrosine residues are shown to highlight their positioning within the trimer. Residue F100e of 40591-a.01 is also shown since it is similarly inserted into the trimer hole but cannot be modified posttranslationally.

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