Summary
Germline usage, specifically the V-gene, determines whether the CDR3 of nanobodies is kinked or extended (Bahrami (1)). The two most common camelid germlines in the PDB, IGHV3S53 and IGHV3-3, are 75% extended and 82% kinked, respectively. In contrast, J-gene usage had no impact.
Details
As of the 2023 study, all kinked nanobody CDR3s have F37, F47, and mostly Q44, whereas all extended CDR3s have Y37, L47, and non-conserved 44.
Figures
Ref Bahrami (1)
1.
Bahrami Dizicheh Z, Chen I-L, Koenig P. VHH CDR-H3 conformation is determined by VH germline usage. Communications Biology. 2023;6(1). Available from: https://doi.org/10.1038/s42003-023-05241-y