Cryo-EM of mammalian PA28αβ-iCPimmunoproteasome reveals a distinct mechanism of proteasome activation by PA28αβ

The proteasome activator PA28{beta} affects MHC class-I antigen presentation by associating with immunoproteasome core particles (iCPs). However, due to the lack of a mammalian PA28{beta}-iCP structure, how PA28{beta} regulates proteasome remains elusive. Here we present the complete architectures of the mammalian PA28{beta}-iCP immunoproteasome and free iCP at near atomic-resolution by cryo-EM, and determined the spatial arrangement between PA28{beta} and iCP through XL-MS. Our structures revealed a slight leaning of PA28{beta} towards the 3-4 side of iCP, disturbing the allosteric network of the gate-keeper 2/3/4 subunits, resulting in a partial open iCP gate. We found that the binding and activation mechanism of iCP by PA28{beta} is distinct from those of constitutive CP by the homoheptameric TbPA26 or PfPA28. Our study sheds lights on the mechanism of enzymatic activity stimulation of immunoproteasome and suggests that PA28{beta}-iCP has experienced profound remodeling during evolution to achieve its current level of function in immune response.