Structural model of H5 HA bound to tufted duck MHC-II

Below is a structural model of H5 HA bound to tufted duck MHC-II generated using cryo-EM and AlphaFold 3 as described in Dadonaite et al (2026).

In this model, the HA trimer is shown in a surface representation and tufted duck MHC-II is shown as a cartoon. Both HA and the MHC-II are colored by how mutations to them affect binding, with sites colored red when most mutations at decrease binding and blue when most mutations increase binding.

The PDB file for this model is available here and has been submitted to the Protein Data Bank with identifier 36XU.