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. 2013 Jun 3;210(6):1235–1249. doi: 10.1084/jem.20130221

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© 2013 Diskin et al.

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Figure 3. — 45-46m2–gp120 complex structure. (A) 45-46m2/gp120 structure with gp120 as a gray surface and 45-46m2 Fab in cyan (HC) and blue (LC) Cα traces. Ordered N-glycans are shown in van der Waals representation, with the Asn276_gp120–linked N-glycan highlighted in shades of red. The locations of Tyr28_45-46m2(LC) and Trp54_45-46m2(HC) are indicated by arrows. (B) Buried surface areas between gp120 and the indicated antibodies. The buried surface area for NIH45-46^G54W was calculated by adding the contribution of Trp54 (derived from the structure of 45-46m2/gp120) to the buried surface area calculated from the NIH45-46/gp120 structure. (C) Close-up comparison of the interactions of Trp54_45-46m2 (cyan side chain) and Gly54_NIH45-46 (magenta) with gp120 in the structures of 45-46m2/gp120 (gray) and NIH45-46/gp120 (magenta). A hydrogen bond (green dashed line) between the nitrogen atom of the Trp54_45-46m2 indole ring and the main chain carbonyl oxygen of Gly473_gp120 creates a 4 Å shift (black arrow; Cα-Cα distance) of the gp120 main chain toward Trp54_45-46m2, and Ile371_gp120 adopts a different rotamer to accommodate Trp54_45-46m2. (D) Electron density (green mesh; σ = 2) for an N-linked glycan attached to Asn276_gp120. A portion from the final model of the 45-46m2–gp120 complex is superimposed on an F_o-F_c electron density map calculated using the initial model before adding the glycan and after several rounds of simulated annealing refinement. (E) Close-up of the Asn276_gp120–attached glycan and its interactions with the 45-46m2 LC (semitransparent surface). Side chains of Tyr28_45-46m2, Trp65_45-46m2, Arg64_45-46m2, and Tyr89_45-46m2 are shown as sticks.