Extended Data Fig. 8: HSV-2 gB bound by Nb1_gbHSV.
From: A nanobody specific to prefusion glycoprotein B neutralizes HSV-1 and HSV-2
(a) Processing pipeline, outlining individual steps with particle numbers and options used deviating from default settings. Except initial steps using WARP51, all steps were done using CryoSPARC52. (b) 2D classes showing the 10 most populated classes. Blue arrowheads mark the position of Nb1_gbHSV. (c) Fourier shell correlation (FSC) for the density map corresponding to the prefusion structure is shown. Resolution was calculated using an FSC threshold of 0.143. (d) Final map coloured by local resolution (FSC threshold 0.143) using a range of 1.5–4.5 Å. (e) Ribbon rendering of the nanobody bound gB structure, zoomed in on the interaction between Nb1_gbHSV (Nb) and DIV, DI & DIII, DI. Domain numbers are shown in roman numbering. Hydrogen bonds are marked by blue dashed lines with a distance and angle tolerance of 0.400 Å and 20° respectively. Bonds not meeting the precise criteria are shown in orange dotted lines. and amino acid names are given in 3 letter code with the according position. Interacting residues are shown in sticks with atoms shown in blue for nitrogen, red for oxygen and white for hydrogen. Protomers are indicated by lower case letters a-c on domain numbers.
