Extended Data Fig. 3: Sequence identity between Ab1999 and Ab1983 with human V3-glycan bNAbs and prediction of glycan clashes.
a,b. Amino acid sequence alignment of Ab1999 HC with BG18 HC mt (a) and of Ab1999 LC with PCDN.76 UCA LC (b). c. Alignment of the BG505 SOSIP.664 trimer structure (PDB 8FR6) with the Ab1999-RC1 complex to predict potential clashes of Ab1999 with glycans. Potential clashes were primarily observed with glycans at Asn133 and Asn137, involving residues from CDRL1, CDRL2, CDRH2 and CDRH3. Specifically, Asn31 and Asn32 on CDRL1 and G68 on CDRL2 clashed with the N137 glycan, while Y52 on CDRH2 and E100E on CDRH3 showed clashes with the N133 glycan. d. Control TZM-bl assay using a non-neutralizing NHP antibody isolated from one of the WIN332-primed NHPs. e. Amino acid sequence alignment of Ab1983 HC with EPTC112 iGL HC. Dots represent identical amino acids. Dashes represent absent amino acids. f. Alignment of the BG505 SOSIP.664 trimer structure (PDB 8FR6) with the Ab1983-WIN332 complex to predict potential clashes of Ab1983 with glycans. Potential clashes were primarily associated with the N133, N137, and N156 glycans. Specifically, the CDRL2, CDRL3, CDRH1, CDRH2 and CDRH3 regions contributed to these clashes. The V52D in CDRL2 clashed with the N133 glycan. Residues G93, T94, and F95C in CDRL3, as well as Y33 in CDRH1 and Y52 in CDRH2, clashed with the N137 glycan. Furthermore, 15 residues within CDRH1, CDRH3 and framework1 exhibited steric overlap with the N156 glycan.
