NSRRC Activity Report 2023

Life Science 049 Fig. 2 : Detailed interface of RBD/IY-2A and the conformational change of RBD upon IY-2A binding. (a) The IY-2A antibody (heavy chain, dark red; light chain, light red) induces a conformational change in the RBD (gray), creating new neutralizing binding sites. HCDR/LCHR refers to heavy/light chain complementarity determining region. Hydrogen bonds are illustrated with green dashed lines. (b) The superimposition of four copies of the IY-2A-bound RBD (varied pink colors) reveals a consistent conformation in this region. Y369 is depicted as sticks, showing a Cα atom displacement of 7.8 Å from the ACE2-bound WT RBD (PDB 6M0J). (c) Overlaying ten WT RBDs (PDB code: 6M0J, 6ZER, 7M7W, 7R6X, 7R6W, 6W41, 7RKU, and 7JMW, the IS-9A-bound, and the FP-12A-bound RBD structures, in light gray shades) demonstrate a conserved conformation in the 364-376 region (α2 helix and α2-β2 linker) compared to the IY-2A-bound RBD (pink), with Y369 highlighted in sticks. (d) Comparing the WT RBD (PDB 6M0J, gray) with five Omicron RBDs (BA.1: PDB 7XAZ, 7XO6; BA.2: PDB 7XB0, 7ZF7, 7XOC, in different purple shades) and the IY-2A-bound RBD (pink) unveils structural variation in this region. [Reproduced from Ref. 2] Fig. 3 : Overall structure and interaction between HR1 and HR2 of SARS-CoV-2. (a) The three HR1–L6–HR2 molecules are presented in the asymmetric unit. (b) The hydrophobic interaction between HR1 and HR2 of SARS-CoV-2 and SARS-CoV. It shows that the two complex structures have similar architecture. Residue differences in fusion cores are shown as stick models. [Reproduced from Ref. 1]